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rough-draft_coverage-tracks_timecourse_size-effect.sh
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#!/bin/bash
# rough-draft_coverage-tracks_timecourse_size-effect.sh
# KA
# 2023-0509
cd ~/2022-2023_RRP6-NAB3/results/2023-0215 \
|| echo "cd'ing failed; check on this..."
# mamba create -n coverage_env -c bioconda deeptools # Only if not installed
#LATER Install bowtie2 as well: mamba install -c bioconda bowtie2
#LATER Install samtools as well: mamba install -c bioconda samtools
source activate coverage_env
# Initialize variables, arrays -----------------------------------------------
job_name="rough-draft_coverage-tracks_timecourse_size-effect" # echo "${job_name}"
p_bam="${HOME}/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI" # echo "${p_bam}"
p_bw="${HOME}/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI" # echo "${p_bw}" # ., "${p_bw}"
p_eo="${p_bw}/err_out" # echo "${p_eo}"
err_out="${p_eo}/${job_name}" # echo "${err_out}"
threads=8 # echo "${threads}"
# Variables for blacklisting
# p_excl="/home/kalavatt/2022-2023_RRP6-NAB3_2023-0215/outfiles_gtf-gff3/already"
# f_excl="SC_features-rRNA-tRNA.bed"
# do_blacklist=FALSE
# blacklist="${p_excl}/${f_excl}"
# Timecourse samples (calculated values described below)
unset a_bam
typeset -A a_bam=(
["${p_bam}/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSm2_rep1_tech1___1.7599208"
["${p_bam}/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSm2_rep2_tech1___2.2889032"
["${p_bam}/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp2_rep1_tech1___1.2338584"
["${p_bam}/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp2_rep2_tech1___1.1810227"
["${p_bam}/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp24_rep1_tech1___0.8081369"
["${p_bam}/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp24_rep2_tech1___0.7898672"
["${p_bam}/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp48_rep1_tech1___0.5904367"
["${p_bam}/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp48_rep1_tech2___0.5742435"
["${p_bam}/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp48_rep2_tech1___0.8004773"
["${p_bam}/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6n_DSm2_rep1_tech1___1.5838222"
["${p_bam}/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6n_DSm2_rep2_tech1___1.2963194"
["${p_bam}/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6n_DSp2_rep1_tech1___1.0055450"
["${p_bam}/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6n_DSp2_rep2_tech1___0.9844227"
["${p_bam}/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6n_DSp24_rep1_tech1___1.1520234"
["${p_bam}/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6n_DSp24_rep2_tech1___0.8236362"
["${p_bam}/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6n_DSp48_rep1_tech1___0.7057575"
["${p_bam}/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6n_DSp48_rep2_tech1___0.6738932"
)
unset strand
typeset -a strand=("forward" "reverse")
# echo_test "${strand[@]}"
# Create outdirectories if not present ---------------------------------------
if [[ ! -d "${p_bw}/timecourse_rrp6_wt_size-factor-scaled" ]]; then
mkdir -p "${p_bw}/timecourse_rrp6_wt_size-factor-scaled"
fi
if [[ ! -d "${p_eo}" ]]; then mkdir -p "${p_eo}"; fi
for i in "${!a_bam[@]}"; do
for j in "${strand[@]}"; do
if [[ "${j}" == "forward" ]]; then
ext="m.bw"
elif [[ "${j}" == "reverse" ]]; then
ext="p.bw"
fi
in="${i}"
coef="${a_bam[${i}]#*___}"
out="${a_bam[${i}]%___*}_gsf-${coef}.${ext}"
filter="${j}"
echo "# -------------------------------------"
., ${in}
echo """
in (key) ${in}
out (value) ${out}
scale factor ${coef}
strand ${filter}"""
echo """
sbatch \\
--job-name=\"${job_name}\" \\
--nodes=1 \\
--cpus-per-task=\"${threads}\" \\
--error=\"${err_out}.%A.stderr.txt\" \\
--output=\"${err_out}.%A.stdout.txt\" \\
bamCoverage \\
--bam \"${in}\" \\
--numberOfProcessors \"${threads}\" \\
--binSize 1 \\
--scaleFactor \"${coef}\" \\
--filterRNAstrand=\"${filter}\" \\
--outFileName \"${out}\"
"""
sbatch \
--job-name="${job_name}" \
--nodes=1 \
--cpus-per-task="${threads}" \
--error="${err_out}.%A.stderr.txt" \
--output="${err_out}.%A.stdout.txt" \
bamCoverage \
--bam "${in}" \
--numberOfProcessors "${threads}" \
--binSize 1 \
--scaleFactor "${coef}" \
--filterRNAstrand="${filter}" \
--outFileName "${out}"
sleep 0.33
echo ""
done
done
# From RStudio:
# > # Size factors calculated with respect to all 17 samples
# > dds$sizeFactor %>% as.data.frame()
# .
# WT_DSm2_rep1_tech1 0.5682074
# WT_DSm2_rep2_tech1 0.4368905
# WT_DSp2_rep1_tech1 0.8104658
# WT_DSp2_rep2_tech1 0.8467238
# WT_DSp24_rep1_tech1 1.2374142
# WT_DSp24_rep2_tech1 1.2660357
# WT_DSp48_rep1_tech1 1.6936618
# WT_DSp48_rep1_tech2 1.7414215
# WT_DSp48_rep2_tech1 1.2492546
# r6n_DSm2_rep1_tech1 0.6313840
# r6n_DSm2_rep2_tech1 0.7714148
# r6n_DSp2_rep1_tech1 0.9944856
# r6n_DSp2_rep2_tech1 1.0158238
# r6n_DSp24_rep1_tech1 0.8680379
# r6n_DSp24_rep2_tech1 1.2141282
# r6n_DSp48_rep1_tech1 1.4169173
# r6n_DSp48_rep2_tech1 1.4839146
#
# > # And the reciprocal...
# > (1 / dds$sizeFactor) %>% as.data.frame()
# .
# WT_DSm2_rep1_tech1 1.7599208
# WT_DSm2_rep2_tech1 2.2889032
# WT_DSp2_rep1_tech1 1.2338584
# WT_DSp2_rep2_tech1 1.1810227
# WT_DSp24_rep1_tech1 0.8081369
# WT_DSp24_rep2_tech1 0.7898672
# WT_DSp48_rep1_tech1 0.5904367
# WT_DSp48_rep1_tech2 0.5742435
# WT_DSp48_rep2_tech1 0.8004773
# r6n_DSm2_rep1_tech1 1.5838222
# r6n_DSm2_rep2_tech1 1.2963194
# r6n_DSp2_rep1_tech1 1.0055450
# r6n_DSp2_rep2_tech1 0.9844227
# r6n_DSp24_rep1_tech1 1.1520234
# r6n_DSp24_rep2_tech1 0.8236362
# r6n_DSp48_rep1_tech1 0.7057575
# r6n_DSp48_rep2_tech1 0.6738932
# The job submission...
# ❯ for i in "${!a_bam[@]}"; do
# > for j in "${strand[@]}"; do
# > if [[ "${j}" == "forward" ]]; then
# > ext="m.bw"
# > elif [[ "${j}" == "reverse" ]]; then
# > ext="p.bw"
# > fi
# >
# > in="${i}"
# > coef="${a_bam[${i}]#*___}"
# > out="${a_bam[${i}]%___*}_gsf-${coef}.${ext}"
# > filter="${j}"
# >
# > echo "# -------------------------------------"
# >
# > ., ${in}
# > echo """
# > in (key) ${in}
# > out (value) ${out}
# > scale factor ${coef}
# > strand ${filter}"""
# >
# > echo """
# > sbatch \\
# > --job-name=\"${job_name}\" \\
# > --nodes=1 \\
# > --cpus-per-task=\"${threads}\" \\
# > --error=\"${err_out}.%A.stderr.txt\" \\
# > --output=\"${err_out}.%A.stdout.txt\" \\
# > bamCoverage \\
# > --bam \"${in}\" \\
# > --numberOfProcessors \"${threads}\" \\
# > --binSize 1 \\
# > --scaleFactor \"${coef}\" \\
# > --filterRNAstrand=\"${filter}\" \\
# > --outFileName \"${out}\"
# > """
# >
# > sbatch \
# > --job-name="${job_name}" \
# > --nodes=1 \
# > --cpus-per-task="${threads}" \
# > --error="${err_out}.%A.stderr.txt" \
# > --output="${err_out}.%A.stdout.txt" \
# > bamCoverage \
# > --bam "${in}" \
# > --numberOfProcessors "${threads}" \
# > --binSize 1 \
# > --scaleFactor "${coef}" \
# > --filterRNAstrand="${filter}" \
# > --outFileName "${out}"
# > sleep 0.33
# > echo ""
# > done
# > done
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 102 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp7_DSp24_5782_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp24_rep2_tech1_gsf-0.7898672.m.bw
# scale factor 0.7898672
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.7898672" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp24_rep2_tech1_gsf-0.7898672.m.bw"
#
# Submitted batch job 20186392
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 102 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp7_DSp24_5782_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp24_rep2_tech1_gsf-0.7898672.p.bw
# scale factor 0.7898672
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.7898672" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp24_rep2_tech1_gsf-0.7898672.p.bw"
#
# Submitted batch job 20186393
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM4_DSp2_5781_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp2_rep1_tech1_gsf-1.2338584.m.bw
# scale factor 1.2338584
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.2338584" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp2_rep1_tech1_gsf-1.2338584.m.bw"
#
# Submitted batch job 20186394
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM4_DSp2_5781_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp2_rep1_tech1_gsf-1.2338584.p.bw
# scale factor 1.2338584
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.2338584" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp2_rep1_tech1_gsf-1.2338584.p.bw"
#
# Submitted batch job 20186395
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp6_DSp2_7078_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp2_rep1_tech1_gsf-1.0055450.m.bw
# scale factor 1.0055450
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.0055450" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp2_rep1_tech1_gsf-1.0055450.m.bw"
#
# Submitted batch job 20186396
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp6_DSp2_7078_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp2_rep1_tech1_gsf-1.0055450.p.bw
# scale factor 1.0055450
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.0055450" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp2_rep1_tech1_gsf-1.0055450.p.bw"
#
# Submitted batch job 20186397
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 107 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM10_DSp48_5781_new_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep1_tech2_gsf-0.5742435.m.bw
# scale factor 0.5742435
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.5742435" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep1_tech2_gsf-0.5742435.m.bw"
#
# Submitted batch job 20186398
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 107 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM10_DSp48_5781_new_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep1_tech2_gsf-0.5742435.p.bw
# scale factor 0.5742435
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.5742435" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep1_tech2_gsf-0.5742435.p.bw"
#
# Submitted batch job 20186399
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 103 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM12_DSp48_7079_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp48_rep2_tech1_gsf-0.6738932.m.bw
# scale factor 0.6738932
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.6738932" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp48_rep2_tech1_gsf-0.6738932.m.bw"
#
# Submitted batch job 20186400
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 103 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM12_DSp48_7079_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp48_rep2_tech1_gsf-0.6738932.p.bw
# scale factor 0.6738932
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.6738932" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp48_rep2_tech1_gsf-0.6738932.p.bw"
#
# Submitted batch job 20186401
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 102 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM7_DSp24_5781_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp24_rep1_tech1_gsf-0.8081369.m.bw
# scale factor 0.8081369
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.8081369" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp24_rep1_tech1_gsf-0.8081369.m.bw"
#
# Submitted batch job 20186402
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 102 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM7_DSp24_5781_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp24_rep1_tech1_gsf-0.8081369.p.bw
# scale factor 0.8081369
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.8081369" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp24_rep1_tech1_gsf-0.8081369.p.bw"
#
# Submitted batch job 20186403
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp4_DSp2_5782_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp2_rep2_tech1_gsf-1.1810227.m.bw
# scale factor 1.1810227
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.1810227" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp2_rep2_tech1_gsf-1.1810227.m.bw"
#
# Submitted batch job 20186404
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp4_DSp2_5782_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp2_rep2_tech1_gsf-1.1810227.p.bw
# scale factor 1.1810227
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.1810227" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp2_rep2_tech1_gsf-1.1810227.p.bw"
#
# Submitted batch job 20186405
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 102 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp9_DSp24_7078_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp24_rep1_tech1_gsf-1.1520234.m.bw
# scale factor 1.1520234
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.1520234" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp24_rep1_tech1_gsf-1.1520234.m.bw"
#
# Submitted batch job 20186406
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 102 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp9_DSp24_7078_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp24_rep1_tech1_gsf-1.1520234.p.bw
# scale factor 1.1520234
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.1520234" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp24_rep1_tech1_gsf-1.1520234.p.bw"
#
# Submitted batch job 20186407
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 103 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM10_DSp48_5781_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep1_tech1_gsf-0.5904367.m.bw
# scale factor 0.5904367
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.5904367" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep1_tech1_gsf-0.5904367.m.bw"
#
# Submitted batch job 20186408
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 103 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM10_DSp48_5781_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep1_tech1_gsf-0.5904367.p.bw
# scale factor 0.5904367
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.5904367" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep1_tech1_gsf-0.5904367.p.bw"
#
# Submitted batch job 20186409
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 103 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp10_DSp48_5782_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep2_tech1_gsf-0.8004773.m.bw
# scale factor 0.8004773
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.8004773" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep2_tech1_gsf-0.8004773.m.bw"
#
# Submitted batch job 20186410
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 103 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp10_DSp48_5782_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep2_tech1_gsf-0.8004773.p.bw
# scale factor 0.8004773
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.8004773" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSp48_rep2_tech1_gsf-0.8004773.p.bw"
#
# Submitted batch job 20186411
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 103 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp12_DSp48_7078_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp48_rep1_tech1_gsf-0.7057575.m.bw
# scale factor 0.7057575
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.7057575" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp48_rep1_tech1_gsf-0.7057575.m.bw"
#
# Submitted batch job 20186412
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 103 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp12_DSp48_7078_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp48_rep1_tech1_gsf-0.7057575.p.bw
# scale factor 0.7057575
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.7057575" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp48_rep1_tech1_gsf-0.7057575.p.bw"
#
# Submitted batch job 20186413
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 102 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM9_DSp24_7079_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp24_rep2_tech1_gsf-0.8236362.m.bw
# scale factor 0.8236362
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.8236362" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp24_rep2_tech1_gsf-0.8236362.m.bw"
#
# Submitted batch job 20186414
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 102 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM9_DSp24_7079_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp24_rep2_tech1_gsf-0.8236362.p.bw
# scale factor 0.8236362
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "0.8236362" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp24_rep2_tech1_gsf-0.8236362.p.bw"
#
# Submitted batch job 20186415
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp3_DSm2_7078_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSm2_rep1_tech1_gsf-1.5838222.m.bw
# scale factor 1.5838222
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.5838222" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSm2_rep1_tech1_gsf-1.5838222.m.bw"
#
# Submitted batch job 20186416
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp3_DSm2_7078_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSm2_rep1_tech1_gsf-1.5838222.p.bw
# scale factor 1.5838222
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.5838222" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSm2_rep1_tech1_gsf-1.5838222.p.bw"
#
# Submitted batch job 20186417
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM1_DSm2_5781_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSm2_rep1_tech1_gsf-1.7599208.m.bw
# scale factor 1.7599208
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.7599208" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSm2_rep1_tech1_gsf-1.7599208.m.bw"
#
# Submitted batch job 20186418
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM1_DSm2_5781_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSm2_rep1_tech1_gsf-1.7599208.p.bw
# scale factor 1.7599208
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.7599208" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSm2_rep1_tech1_gsf-1.7599208.p.bw"
#
# Submitted batch job 20186419
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM3_DSm2_7079_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSm2_rep2_tech1_gsf-1.2963194.m.bw
# scale factor 1.2963194
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.2963194" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSm2_rep2_tech1_gsf-1.2963194.m.bw"
#
# Submitted batch job 20186420
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM3_DSm2_7079_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSm2_rep2_tech1_gsf-1.2963194.p.bw
# scale factor 1.2963194
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "1.2963194" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSm2_rep2_tech1_gsf-1.2963194.p.bw"
#
# Submitted batch job 20186421
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp1_DSm2_5782_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSm2_rep2_tech1_gsf-2.2889032.m.bw
# scale factor 2.2889032
# strand forward
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "2.2889032" \
# --filterRNAstrand="forward" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSm2_rep2_tech1_gsf-2.2889032.m.bw"
#
# Submitted batch job 20186422
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/Bp1_DSm2_5782_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSm2_rep2_tech1_gsf-2.2889032.p.bw
# scale factor 2.2889032
# strand reverse
#
# sbatch \
# --job-name="rough-draft_coverage-tracks_timecourse_size-effect" \
# --nodes=1 \
# --cpus-per-task="8" \
# --error="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stderr.txt" \
# --output="/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/err_out/rough-draft_coverage-tracks_timecourse_size-effect.%A.stdout.txt" \
# bamCoverage \
# --bam "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam" \
# --numberOfProcessors "8" \
# --binSize 1 \
# --scaleFactor "2.2889032" \
# --filterRNAstrand="reverse" \
# --outFileName "/home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/WT_DSm2_rep2_tech1_gsf-2.2889032.p.bw"
#
# Submitted batch job 20186423
#
# # -------------------------------------
# lrwxrwxrwx 1 kalavatt 101 Mar 15 16:09 /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam -> ../../../2023-0115/bams_UMI-dedup/aligned_UT_primary_dedup-UMI/BM6_DSp2_7079_UT.primary.dedup-UMI.bam
#
# in (key) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam
# out (value) /home/kalavatt/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI/timecourse_rrp6_wt/r6n_DSp2_rep2_tech1_gsf-0.9844227.m.bw
# scale factor 0.9844227
# strand forward
#
# sbatch \