From 3a9ec8935be71376a5f7209a5f100b25413f34a8 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Thu, 11 Jun 2020 21:04:24 +0200
Subject: [PATCH] Set appropriate parameter. Fixes #83
---
workflow/rules/paired_end.snakefile.smk | 2 +-
workflow/rules/single_end.snakefile.smk | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index d7f40dd..d66b120 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -228,7 +228,7 @@ rule pe_map_genome_star:
--readFilesCommand zcat \
--outSAMunmapped None \
--outFilterMultimapNmax {params.multimappers} \
- --outFilterMultimapScoreRange 1 \
+ --outFilterMultimapScoreRange 0 \
--outFileNamePrefix {params.outFileNamePrefix} \
--outSAMattributes All \
--outStd BAM_SortedByCoordinate \
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index df41f96..0aac065 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -182,7 +182,7 @@ rule map_genome_star:
--readFilesCommand zcat \
--outSAMunmapped None \
--outFilterMultimapNmax {params.multimappers} \
- --outFilterMultimapScoreRange 1 \
+ --outFilterMultimapScoreRange 0 \
--outFileNamePrefix {params.outFileNamePrefix} \
--outSAMattributes All \
--outStd BAM_SortedByCoordinate \
--
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