From 54d37c8ffd1db2c820385c18c3ea86c73be33631 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 20 Jun 2023 11:35:55 +0200
Subject: [PATCH] Only one config for normalizers.
This applies for both bigwig files and RPM-based stuff, and maybe
also for other outputs.
---
small_RNA-seq/small_RNA-seq.snakefile | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index cad4927..a397d52 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -515,9 +515,10 @@ TESTED_SIZE_FACTORS = ["mapped", "non_structural", "all_sisiuRNA", "piRNA", "miR
# and then substraction of a pseudocount, in order to deal with zero counts.
# This seems to perform well (see "test_size_factor" results).
DE_SIZE_FACTORS = ["non_structural", "median_ratio_to_pseudo_ref"]
-SIZE_FACTORS = ["non_structural", "piRNA"]
+SIZE_FACTORS = config.get("size_factors", ["non_structural"])
#NORMALIZER = "median_ratio_to_pseudo_ref"
-RPM_NORMS = config.get("rpm_norms", SIZE_FACTORS)
+# Do we really need distinct lists of normalizers?
+RPM_NORMS = SIZE_FACTORS
RPM_FOLD_TYPES = [
f"mean_log2_RPM_by_{norm}_fold"
for norm in RPM_NORMS]
--
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