End-of-day push, 2023-0908: Have updated scripts in 2023-0215 to use …

…new repo name in work-directory path, and have begun writing to-be-determined.R to implement JM's method for estimating total RNA between Q and G1, and Q and log
kalavattam · Sep 9, 2023 · 53b7a51 · 53b7a51
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diff --git a/results/2023-0215/rough-draft_coverage-tracks.sh b/results/2023-0215/rough-draft_coverage-tracks.sh
@@ -6,7 +6,7 @@
 
 
 #  Run grabnode with defaults except request 8 nodes
-cd ~/2022_transcriptome-construction/results/2023-0215 \
+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
@@ -18,16 +18,16 @@ source activate coverage_env
 #  Initialize variables, arrays -----------------------------------------------
 job_name="rough-draft_coverage-tracks"
 
-p_bam="${HOME}/2022_transcriptome-construction/results/2023-0215/bams_renamed/UT_prim_UMI"  # ., "${p_bam}"
-p_bw="${HOME}/2022_transcriptome-construction/results/2023-0215/bws/UT_prim_UMI"  # ., "${p_bw}"
+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_transcriptome-construction_2023-0215/outfiles_gtf-gff3/already"  # ., "${p_excl}"
+p_excl="/home/kalavatt/2022-2023_RRP6-NAB3_2023-0215/outfiles_gtf-gff3/already"  # ., "${p_excl}"
 # f_excl="SC_features-rRNA-tRNA.bed"
 f_excl="SC_features-rRNA-tRNA_intergenic-MEP2-AAH1.bed"
 # do_blacklist=FALSE

diff --git a/results/2023-0215/rough-draft_coverage-tracks_timecourse_size-effect.sh b/results/2023-0215/rough-draft_coverage-tracks_timecourse_size-effect.sh
diff --git a/results/2023-0215/rough-draft_draw_scatter-plots.R b/results/2023-0215/rough-draft_draw_scatter-plots.R
@@ -485,7 +485,7 @@ theme_AG_boxed_no_legend <- theme_AG_boxed + theme(legend.position = "none")
 #  Get situated, load RDS files ===============================================
 #  Set work dir
 p_base <- "/Users/kalavatt/projects-etc"
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 setwd(paste(p_base, p_exp, sep = "/"))
 

diff --git a/results/2023-0215/rough-draft_estimate-RNA-degredation.R b/results/2023-0215/rough-draft_estimate-RNA-degredation.R
@@ -136,7 +136,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_base <- "/Users/kalavatt/projects-etc"
 }
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 #  Set work dir
 paste(p_base, p_exp, sep = "/") %>% setwd()

diff --git a/results/2023-0215/rough-draft_evaluate-categories_expression.R b/results/2023-0215/rough-draft_evaluate-categories_expression.R
@@ -37,7 +37,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_local <- "/Users/kalavatt/projects-etc"
 }
-p_wd <- "2022_transcriptome-construction/results/2023-0215"
+p_wd <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 setwd(paste(p_local, p_wd, sep = "/"))
 getwd()

diff --git a/results/2023-0215/rough-draft_evaluate-categories_expression_initial.Rmd b/results/2023-0215/rough-draft_evaluate-categories_expression_initial.Rmd
@@ -32,7 +32,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_local <- "/Users/kalavatt/projects-etc"
 }
-p_wd <- "2022_transcriptome-construction/results/2023-0215"
+p_wd <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 setwd(paste(p_local, p_wd, sep = "/"))
 getwd()
@@ -185,7 +185,7 @@ underscore$`n3-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1` %>% sum()  # [1] 21827889
 grabnode  # 1 CPU, defaults
 ml SAMtools/1.16.1-GCC-11.2.0
 
-cd /home/kalavatt/tsukiyamalab/kalavatt/2022_transcriptome-construction \
+cd /home/kalavatt/tsukiyamalab/kalavatt/2022-2023_RRP6-NAB3 \
     || echo "cd'ing failed; check on this"
 
 cd results/2023-0215/bams_renamed/UT_prim_UMI \

diff --git a/results/2023-0215/rough-draft_handle-matrices-gtfs.R b/results/2023-0215/rough-draft_handle-matrices-gtfs.R
@@ -11,7 +11,7 @@
 # library(rtracklayer)
 # library(tidyverse)
 # 
-# setwd("~/projects-etc/2022_transcriptome-construction/results/2023-0215")
+# setwd("~/projects-etc/2022-2023_RRP6-NAB3/results/2023-0215")
 # getwd()
 # 
 # list.dirs()
@@ -37,7 +37,7 @@ library(GenomicRanges)
 library(rtracklayer)
 library(tidyverse)
 
-setwd("~/projects-etc/2022_transcriptome-construction/results/2023-0215")
+setwd("~/projects-etc/2022-2023_RRP6-NAB3/results/2023-0215")
 getwd()
 
 t_mat <- "all-samples.combined-SC-KL-20S.hc-strd-eq.mRNA.tsv"
@@ -166,7 +166,7 @@ library(GenomicRanges)
 library(rtracklayer)
 library(tidyverse)
 
-setwd("~/projects-etc/2022_transcriptome-construction/results/2023-0215")
+setwd("~/projects-etc/2022-2023_RRP6-NAB3/results/2023-0215")
 getwd()
 
 t_mat <- "all-samples.combined-AG.hc-strd-eq.XUT.tsv"

diff --git a/results/2023-0215/rough-draft_handle-tables_establish-study-design.R b/results/2023-0215/rough-draft_handle-tables_establish-study-design.R
@@ -27,7 +27,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_local <- "/Users/kalavatt/projects-etc"
 }
-p_wd <- "2022_transcriptome-construction/results/2023-0215"
+p_wd <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 setwd(paste(p_local, p_wd, sep = "/"))
 getwd()

diff --git a/results/2023-0215/rough-draft_new-approach-to-analyses.R b/results/2023-0215/rough-draft_new-approach-to-analyses.R
@@ -1628,7 +1628,7 @@ theme_AG_boxed_no_legend <- theme_AG_boxed + theme(legend.position = "none")
 
 #  Get situated, load counts matrix ===========================================
 p_base <- "/Users/kalavatt/projects-etc"
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 #  Set work dir
 paste(p_base, p_exp, sep = "/") %>% setwd()

diff --git a/results/2023-0215/rough-draft_plot-TPM_N-varies-on-SS_LFC-varies-on-TPM.R b/results/2023-0215/rough-draft_plot-TPM_N-varies-on-SS_LFC-varies-on-TPM.R
@@ -779,7 +779,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_base <- "/Users/kalavatt/projects-etc"
 }
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 paste(p_base, p_exp, sep = "/") %>% setwd()
 

diff --git a/results/2023-0215/rough-draft_plot-distributions_expression.R b/results/2023-0215/rough-draft_plot-distributions_expression.R
@@ -128,7 +128,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_base <- "/Users/kalavatt/projects-etc"
 }
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 #  Set work dir
 paste(p_base, p_exp, sep = "/") %>% setwd()

diff --git a/results/2023-0215/rough-draft_plot-distributions_length.R b/results/2023-0215/rough-draft_plot-distributions_length.R
@@ -125,7 +125,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_base <- "/Users/kalavatt/projects-etc"
 }
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 #  Set work dir
 paste(p_base, p_exp, sep = "/") %>% setwd()

diff --git a/results/2023-0215/rough-draft_run-analyses_Fig-5B-5C.R b/results/2023-0215/rough-draft_run-analyses_Fig-5B-5C.R
@@ -70,7 +70,7 @@ theme_AG_boxed_no_legend <- theme_AG_boxed + theme(legend.position = "none")
 #  Get situated, load RDS files, and load TPM dataframe =======================
 #  Set work dir
 p_base <- "/Users/kalavatt/projects-etc"
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 paste(p_base, p_exp, sep = "/") %>% setwd()
 

diff --git a/results/2023-0215/rough-draft_run-analyses_GO.R b/results/2023-0215/rough-draft_run-analyses_GO.R
@@ -138,7 +138,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_base <- "/Users/kalavatt/projects-etc"
 }
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 #  Set work dir
 paste(p_base, p_exp, sep = "/") %>% setwd()

diff --git a/results/2023-0215/rough-draft_run-analyses_rlog-PCA_write-rds.R b/results/2023-0215/rough-draft_run-analyses_rlog-PCA_write-rds.R
@@ -985,7 +985,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_base <- "/Users/kalavatt/projects-etc"
 }
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 #  Set work dir
 paste(p_base, p_exp, sep = "/") %>% setwd()

diff --git a/results/2023-0215/rough-draft_timecourse-samples_processing_part-1a.R b/results/2023-0215/rough-draft_timecourse-samples_processing_part-1a.R
@@ -698,7 +698,7 @@ theme_slick_no_legend <- theme_slick + theme(legend.position = "none")
 
 #  Get situated, load counts matrix ===========================================
 p_base <- "/Users/kalavatt/projects-etc"
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 p_tsv <- "outfiles_htseq-count/already/combined-SC-KL-20S/UT_prim_UMI"
 f_tsv <- "all-samples.combined-SC-KL-20S.hc-strd-eq.mRNA.tsv"
 # paste(p_base, p_exp, p_tsv, f_tsv, sep = "/") %>%

diff --git a/results/2023-0215/rough-draft_timecourse-samples_processing_part-1b.R b/results/2023-0215/rough-draft_timecourse-samples_processing_part-1b.R
@@ -698,7 +698,7 @@ theme_slick_no_legend <- theme_slick + theme(legend.position = "none")
 
 #  Get situated, load counts matrix ===========================================
 p_base <- "/Users/kalavatt/projects-etc"
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 p_tsv <- "outfiles_htseq-count/already/combined-SC-KL-20S/UT_prim_UMI"
 f_tsv <- "all-samples.combined-SC-KL-20S.hc-strd-eq.mRNA.tsv"
 # paste(p_base, p_exp, p_tsv, f_tsv, sep = "/") %>%

diff --git a/results/2023-0215/rough-draft_timecourse-samples_processing_part-1c.R b/results/2023-0215/rough-draft_timecourse-samples_processing_part-1c.R
@@ -700,7 +700,7 @@ theme_slick_no_legend <- theme_slick + theme(legend.position = "none")
 
 #  Get situated, load counts matrix ===========================================
 p_base <- "/Users/kalavatt/projects-etc"
-p_exp <- "2022_transcriptome-construction/results/2023-0215"
+p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
 p_tsv <- "outfiles_htseq-count/already/combined-SC-KL-20S/UT_prim_UMI"
 f_tsv <- "all-samples.combined-SC-KL-20S.hc-strd-eq.mRNA.tsv"
 # paste(p_base, p_exp, p_tsv, f_tsv, sep = "/") %>%

diff --git a/results/2023-0215/rough-draft_write-gtf-blacklist.R b/results/2023-0215/rough-draft_write-gtf-blacklist.R
@@ -17,7 +17,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_local <- "/Users/kalavatt/projects-etc"
 }
-p_wd <- "2022_transcriptome-construction/results/2023-0215"
+p_wd <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 setwd(paste(p_local, p_wd, sep = "/"))
 getwd()

diff --git a/results/2023-0215/run_chi-sq_quantile-filtered-coding-assignments.R b/results/2023-0215/run_chi-sq_quantile-filtered-coding-assignments.R
@@ -12,7 +12,7 @@ if(stringr::str_detect(getwd(), "kalavattam")) {
 } else {
     p_local <- "/Users/kalavatt/projects-etc"
 }
-p_wd <- "2022_transcriptome-construction/results/2023-0215"
+p_wd <- "2022-2023_RRP6-NAB3/results/2023-0215"
 
 setwd(p_wd)
 # getwd()