From 783a77ace44d06be9deaac0e432a4037daf2ba8d Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Mon, 10 Feb 2020 12:42:34 +0100 Subject: [PATCH] Compute TPM and "efficiencies" on protein_coding. --- Degradome-seq/Degradome-seq.snakefile | 2 +- PRO-seq/PRO-seq.snakefile | 2 +- RNA_Seq_Cecere/RNA-seq.snakefile | 2 +- Ribo-seq/Ribo-seq.snakefile | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile index ccd8c38..3d1b6e5 100644 --- a/Degradome-seq/Degradome-seq.snakefile +++ b/Degradome-seq/Degradome-seq.snakefile @@ -130,7 +130,7 @@ rule all: # lib=LIBS, biotype=["alltypes"], orientation=ORIENTATIONS), expand( OPJ(counts_dir, "diff_%s" % eff_name, "{contrast}", "{orientation}_{biotype}", "{contrast}_diff_%s.txt" % eff_name), - contrast=DD_CONTRASTS, orientation=["fwd"], biotype=["alltypes"]), + contrast=DD_CONTRASTS, orientation=["fwd"], biotype=["alltypes", "protein_coding"]), include: ensure_relative(irules["link_raw_data"], workflow.basedir) diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile index f8717af..9c290c9 100644 --- a/PRO-seq/PRO-seq.snakefile +++ b/PRO-seq/PRO-seq.snakefile @@ -357,7 +357,7 @@ rule all: expand(OPJ( "{trimmer}", aligner, "mapped_C_elegans", "{counter}", "all_on_C_elegans", "{biotype}_{orientation}_TPM.txt"), - trimmer=TRIMMERS, counter=COUNTERS, biotype=["alltypes"], orientation=ORIENTATIONS), + trimmer=TRIMMERS, counter=COUNTERS, biotype=["alltypes", "protein_coding"], orientation=ORIENTATIONS), #expand(OPJ("{trimmer}", "figures", aligner, "{lib}_mean", "{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)), trimmer=TRIMMERS, lib=LIBS, orientation=["all"], biotype=["protein_coding"]), #expand(OPJ("{trimmer}", "figures", aligner, "{lib}_mean", "{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)), trimmer=TRIMMERS, lib=LIBS, orientation=["all"], biotype=METAGENE_BIOTYPES), # TODO: Add metagene profiles similar to small RNA-seq diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile index a420f59..0853fde 100644 --- a/RNA_Seq_Cecere/RNA-seq.snakefile +++ b/RNA_Seq_Cecere/RNA-seq.snakefile @@ -318,7 +318,7 @@ counts_files = [ OPJ(aligner, f"mapped_{genome}", "{counter}", "all_{mapped_type}", "{biotype}_{orientation}_TPM.txt"), counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"], - biotype=["alltypes"], orientation=ORIENTATIONS), + biotype=["alltypes", "protein_coding"], orientation=ORIENTATIONS), expand( OPJ(aligner, f"mapped_{genome}", "{counter}", "all_{mapped_type}", "{biotype}_{orientation}_RPK.txt"), diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile index f48f972..7e60128 100644 --- a/Ribo-seq/Ribo-seq.snakefile +++ b/Ribo-seq/Ribo-seq.snakefile @@ -579,7 +579,7 @@ rule all: # translation_efficiency expand( OPJ(counts_dir, "{lib}_mean_{read_type}_on_%s" % genome, "{lib}_{biotype}_{orientation}_%s.txt" % eff_name), - lib=EFF_LIBS, read_type=["RPF"], biotype=["alltypes"], orientation=["fwd"]), + lib=EFF_LIBS, read_type=["RPF"], biotype=["alltypes", "protein_coding"], orientation=["fwd"]), # DESeq2 results expand( OPJ( @@ -599,7 +599,7 @@ rule all: counts_dir, "diff_%s_{read_type}" % eff_name, "{contrast}", "{orientation}_{biotype}", "{contrast}_diff_%s.txt" % eff_name), - read_type=["RPF"], contrast=DT_CONTRASTS, orientation=["fwd"], biotype=["alltypes"]), + read_type=["RPF"], contrast=DT_CONTRASTS, orientation=["fwd"], biotype=["alltypes", "protein_coding"]), # rule future_all: # meta_profiles, -- GitLab