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rough-draft_coverage-tracks.sh
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#!/bin/bash
# rough-draft_coverage-tracks.sh
# KA
# 2023-0403-0404-0704
# Run grabnode with defaults except request 8 nodes
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
#TODO #LATER Install bowtie2 as well: mamba install -c bioconda bowtie2
#TODO #LATER Install samtools as well: mamba install -c bioconda samtools
source activate coverage_env
# Initialize variables, arrays -----------------------------------------------
job_name="rough-draft_coverage-tracks"
p_bam="${HOME}/2022-2023_RRP6-NAB3/results/2023-0215/bams_renamed/UT_prim_UMI" # ., "${p_bam}"
p_bw="${HOME}/2022-2023_RRP6-NAB3/results/2023-0215/bws/UT_prim_UMI" # ., "${p_bw}"
p_eo="${p_bw}/err_out" # ., "${p_eo}"
err_out="${p_eo}/${job_name}" # echo "${err_out}"
# threads="${SLURM_CPUS_ON_NODE}" # echo "${threads}"
threads=8 # echo "${threads}"
p_excl="/home/kalavatt/2022-2023_RRP6-NAB3_2023-0215/outfiles_gtf-gff3/already" # ., "${p_excl}"
# f_excl="SC_features-rRNA-tRNA.bed"
f_excl="SC_features-rRNA-tRNA_intergenic-MEP2-AAH1.bed"
# do_blacklist=FALSE
do_blacklist=TRUE
blacklist="${p_excl}/${f_excl}" # echo "${blacklist}"
unset a_bam
typeset -A a_bam
# samples_figs_1_2
run_samples_figs_1_2=TRUE #ARGUMENT
if [[ "${run_samples_figs_1_2}" == TRUE ]]; then
a_bam["${p_bam}/WT_G1_day1_ovn_N_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/wt_ovn/WT_G1_N_rep1"
a_bam["${p_bam}/WT_G1_day1_ovn_N_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/wt_ovn/WT_G1_N_rep2"
a_bam["${p_bam}/WT_G1_day1_ovn_SS_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/wt_ovn/WT_G1_SS_rep1"
a_bam["${p_bam}/WT_G1_day1_ovn_SS_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/wt_ovn/WT_G1_SS_rep2"
a_bam["${p_bam}/WT_Q_day7_ovn_N_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/wt_ovn/WT_Q_N_rep1"
a_bam["${p_bam}/WT_Q_day7_ovn_N_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/wt_ovn/WT_Q_N_rep2"
a_bam["${p_bam}/WT_Q_day7_ovn_SS_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/wt_ovn/WT_Q_SS_rep1"
a_bam["${p_bam}/WT_Q_day7_ovn_SS_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/wt_ovn/WT_Q_SS_rep2"
fi
# samples_fig_6
run_samples_fig_6=FALSE #ARGUMENT
if [[ "${run_samples_fig_6}" == TRUE ]]; then
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_SS_rep1"
a_bam["${p_bam}/WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSm2_SS_rep2"
a_bam["${p_bam}/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp2_SS_rep1"
a_bam["${p_bam}/WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp2_SS_rep2"
a_bam["${p_bam}/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp24_SS_rep1"
a_bam["${p_bam}/WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp24_SS_rep2"
a_bam["${p_bam}/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp48_SS_rep1"
a_bam["${p_bam}/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp48_SS_rep1"
a_bam["${p_bam}/WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/WT_DSp48_SS_rep2"
a_bam["${p_bam}/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6-n_DSm2_SS_rep1"
a_bam["${p_bam}/r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6-n_DSm2_SS_rep2"
a_bam["${p_bam}/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6-n_DSp2_SS_rep1"
a_bam["${p_bam}/r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6-n_DSp2_SS_rep2"
a_bam["${p_bam}/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6-n_DSp24_SS_rep1"
a_bam["${p_bam}/r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6-n_DSp24_SS_rep2"
a_bam["${p_bam}/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6-n_DSp48_SS_rep1"
a_bam["${p_bam}/r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/timecourse_rrp6_wt/r6-n_DSp48_SS_rep2"
fi
# samples_figs_3_6
run_samples_figs_3_6=FALSE #ARGUMENT
if [[ "${run_samples_figs_3_6}" == TRUE ]]; then
a_bam["${p_bam}/WT_G1_day1_tcn_SS_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/WT_G1_SS_rep1"
a_bam["${p_bam}/WT_G1_day1_tcn_SS_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/WT_G1_SS_rep2"
a_bam["${p_bam}/WT_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/WT_Q_N_rep1"
a_bam["${p_bam}/WT_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/WT_Q_N_rep2"
a_bam["${p_bam}/WT_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/WT_Q_SS_rep1"
a_bam["${p_bam}/WT_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/WT_Q_SS_rep2"
a_bam["${p_bam}/r6-n_G1_day1_tcn_SS_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/r6-n_G1_SS_rep1"
a_bam["${p_bam}/r6-n_G1_day1_tcn_SS_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/r6-n_G1_SS_rep2"
a_bam["${p_bam}/r6-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/r6-n_Q_N_rep1"
a_bam["${p_bam}/r6-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/r6-n_Q_N_rep2"
a_bam["${p_bam}/r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/r6-n_Q_SS_rep1"
a_bam["${p_bam}/r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech2.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/r6-n_Q_SS_rep1"
a_bam["${p_bam}/r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/rrp6_wt/r6-n_Q_SS_rep2"
fi
# samples_fig_4
run_samples_fig_4=FALSE #ARGUMENT
if [[ "${run_samples_fig_4}" == TRUE ]]; then
a_bam["${p_bam}/n3-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/n3-d_Q_N_rep1"
a_bam["${p_bam}/n3-d_Q_day7_tcn_N_aux-T_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/n3-d_Q_N_rep2"
a_bam["${p_bam}/n3-d_Q_day7_tcn_N_aux-T_tc-F_rep3_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/n3-d_Q_N_rep3"
a_bam["${p_bam}/n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/n3-d_Q_SS_rep1"
a_bam["${p_bam}/n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/n3-d_Q_SS_rep2"
a_bam["${p_bam}/n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep3_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/n3-d_Q_SS_rep3"
a_bam["${p_bam}/o-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/o-d_Q_N_rep1"
a_bam["${p_bam}/o-d_Q_day7_tcn_N_aux-T_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/o-d_Q_N_rep2"
a_bam["${p_bam}/o-d_Q_day7_tcn_SS_aux-T_tc-F_rep1_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/o-d_Q_SS_rep1"
a_bam["${p_bam}/o-d_Q_day7_tcn_SS_aux-T_tc-F_rep2_tech1.UT_prim_UMI.bam"]="${p_bw}/nab3_ostir/o-d_Q_SS_rep2"
fi
unset strand
typeset -a strand=("forward" "reverse")
# echo_test "${strand[@]}"
# Create outdirectories if not present ---------------------------------------
if [[ ! -d "${p_bw}" ]]; then mkdir -p ${p_bw}/{wt_ovn,timecourse_rrp6_wt,rrp6_wt,nab3_ostir}; fi
if [[ ! -d "${p_eo}" ]]; then mkdir -p "${p_eo}"; fi
# Check associative array, assignments, commands -----------------------------
for i in "${!a_bam[@]}"; do
for j in "${strand[@]}"; do
if [[ "${do_blacklist}" == FALSE ]]; then
if [[ "${j}" == "forward" ]]; then
ext="TPM.m.bw"
elif [[ "${j}" == "reverse" ]]; then
ext="TPM.p.bw"
fi
in="${i}"
out="${a_bam[${i}]}.${ext}"
filter="${j}"
echo """
., ${in}
in (key) ${in}
out (value) ${out}
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 \"${threads}\" \\
# --binSize 1 \\
# --normalizeUsing BPM \\
# --filterRNAstrand=\"${filter}\" \\
# --outFileName \"${out}\"
# """
elif [[ "${do_blacklist}" == TRUE ]]; then
if [[ "${j}" == "forward" ]]; then
if [[ "${f_excl}" == "SC_features-rRNA-tRNA.bed" ]]; then
ext="bl-TPM.m.bw"
elif [[ "${f_excl}" == "SC_features-rRNA-tRNA_intergenic-MEP2-AAH1.bed" ]]; then
ext="bl-rRNA-tRNA-inter-M2-A1-TPM.m.bw"
fi
elif [[ "${j}" == "reverse" ]]; then
if [[ "${f_excl}" == "SC_features-rRNA-tRNA.bed" ]]; then
ext="bl-TPM.p.bw"
elif [[ "${f_excl}" == "SC_features-rRNA-tRNA_intergenic-MEP2-AAH1.bed" ]]; then
ext="bl-rRNA-tRNA-inter-M2-A1-TPM.p.bw"
fi
fi
in="${i}"
out="${a_bam[${i}]}.${ext}"
filter="${j}"
echo """
., ${in}
in (key) ${in}
out (value) ${out}
strand ${filter}
blacklist ${blacklist}
"""
# echo """
# sbatch \\
# --job-name=\"${job_name}\" \\
# --nodes=1 \\
# --cpus-per-task=\"${threads}\" \\
# --error=\"${err_out}.%A.stderr.txt\" \\
# --output=\"${err_out}.%A.stdout.txt\" \\
# bamCoverage \\
# --bam \"${in}\" \\
# --numberOfProcessors \"${threads}\" \\
# --binSize 1 \\
# --normalizeUsing BPM \\
# --filterRNAstrand=\"${filter}\" \\
# --blackListFileName \"${blacklist}\" \\
# --outFileName \"${out}\"
# """
fi
done
done
# Submit jobs ----------------------------------------------------------------
for i in "${!a_bam[@]}"; do
for j in "${strand[@]}"; do
if [[ "${do_blacklist}" == FALSE ]]; then
if [[ "${j}" == "forward" ]]; then
ext="TPM.m.bw"
elif [[ "${j}" == "reverse" ]]; then
ext="TPM.p.bw"
fi
in="${i}"
out="${a_bam[${i}]}.${ext}"
filter="${j}"
echo """
., ${in}
in (key) ${in}
out (value) ${out}
strand ${filter}
"""
sbatch \
--job-name="${job_name}" \
--nodes=1 \
--cpus-per-task="${threads}" \
--error="${err_out}.%A.stderr.txt" \
--output="${err_out}.%A.stdout.txt" \
bamCoverage \
--bam "${in}" \
--numberOfProcessors "${threads}" \
--binSize 1 \
--normalizeUsing BPM \
--filterRNAstrand="${filter}" \
--outFileName "${out}"
sleep 0.33
elif [[ "${do_blacklist}" == TRUE ]]; then
if [[ "${j}" == "forward" ]]; then
if [[ "${f_excl}" == "SC_features-rRNA-tRNA.bed" ]]; then
ext="bl-TPM.m.bw"
elif [[ "${f_excl}" == "SC_features-rRNA-tRNA_intergenic-MEP2-AAH1.bed" ]]; then
ext="bl-rRNA-tRNA-inter-M2-A1-TPM.m.bw"
fi
elif [[ "${j}" == "reverse" ]]; then
if [[ "${f_excl}" == "SC_features-rRNA-tRNA.bed" ]]; then
ext="bl-TPM.p.bw"
elif [[ "${f_excl}" == "SC_features-rRNA-tRNA_intergenic-MEP2-AAH1.bed" ]]; then
ext="bl-rRNA-tRNA-inter-M2-A1-TPM.p.bw"
fi
fi
in="${i}"
out="${a_bam[${i}]}.${ext}"
filter="${j}"
echo """
., ${in}
in (key) ${in}
out (value) ${out}
strand ${filter}
blacklist ${blacklist}
"""
sbatch \
--job-name="${job_name}" \
--nodes=1 \
--cpus-per-task="${threads}" \
--error="${err_out}.%A.stderr.txt" \
--output="${err_out}.%A.stdout.txt" \
bamCoverage \
--bam "${in}" \
--numberOfProcessors "${threads}" \
--binSize 1 \
--normalizeUsing BPM \
--filterRNAstrand="${filter}" \
--blackListFileName "${blacklist}" \
--outFileName "${out}"
sleep 0.33
fi
done
done
# The --filterRNAstrand "option assumes a standard dUTP-based library
#+ preparation (that is, --filterRNAstrand=forward keeps minus-strand reads,
#+ which originally came from genes on the forward strand using a dUTP-
#+ based method)."
#+
#+ Thus, in our context for RF libraries, --filterRNAstrand=forward gives us
#+ plus-strand reads; --filterRNAstrand=reverse gives us minus-strand reads.
# WARNING Need to double check what was written above; in the code, I'm
#+ assigning "forward" to the minus strand and "reverse" to the plus strand
#DONE For --blackListFileName, make a gtf of rRNA, tRNA, and Ty elements