From 761517da97e9f5cecb96b2e1e24354c63ff9c29a Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Thu, 2 Aug 2018 11:04:10 +0200
Subject: [PATCH] add filtering step of reads based on mapping quality >=2
---
src/RNAseq_sen1D_bowtie2_SE.config | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/src/RNAseq_sen1D_bowtie2_SE.config b/src/RNAseq_sen1D_bowtie2_SE.config
index ce64be9..478c45e 100644
--- a/src/RNAseq_sen1D_bowtie2_SE.config
+++ b/src/RNAseq_sen1D_bowtie2_SE.config
@@ -33,6 +33,9 @@ profiles {
$mapping_fastq {
container = "bowtie2:2.3.4.1"
}
+ $quality_filtered_bam {
+ container = "samtools:1.7"
+ }
$sort_bam {
container = "samtools:1.7"
}
@@ -132,6 +135,9 @@ profiles {
$mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
+ $quality_filtered_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
$sort_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
--
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