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),
-- 
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