From 79f9780b6110cbed599c3d1026fea3f065762588 Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Wed, 22 Jan 2020 11:47:16 +0100 Subject: [PATCH] Output RPM folds for all_si_22G. This is an attempt to generate more interesting output when the genome has extra transgenes. --- small_RNA-seq/small_RNA-seq.snakefile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index 107e1ed..20a77e3 100644 --- a/small_RNA-seq/small_RNA-seq.snakefile +++ b/small_RNA-seq/small_RNA-seq.snakefile @@ -849,6 +849,8 @@ rule all: #expand(OPJ(feature_counts_dir, "summaries", "{lib}_{rep}_nb_non_structural.txt"), filtered_product, lib=LIBS, rep=REPS), #OPJ(mapping_dir, f"RPM_folds_{size_selected}", "all", "pisimi_mean_log2_RPM_fold.txt"), OPJ(mapping_dir, f"RPM_folds_{size_selected}", "all", f"pimi{SI_MIN}G_mean_log2_RPM_fold.txt"), + # To have RPM (folds) for transgenes (which are not in prot_si category) + OPJ(mapping_dir, f"RPM_folds_{size_selected}", "all", f"all_si_{SI_MIN}G_mean_log2_RPM_fold.txt"), # Not looking ad deseq2 results any more #expand(OPJ(mapping_dir, f"deseq2_{size_selected}", "all", "pisimi_{fold_type}.txt"), fold_type=["log2FoldChange"]), #expand(OPJ(mapping_dir, "RPM_folds_%s" % size_selected, "{contrast}", "{contrast}_{small_type}_RPM_folds.txt"), contrast=IP_CONTRASTS, small_type=DE_TYPES), -- GitLab