From bf2153241d9073bf055c419b2589015e38066167 Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Mon, 2 Feb 2015 18:12:28 +0100
Subject: [PATCH] new adapater set for trimming
---
dge_workflow/dge_utils.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index 073092e..4e6cfb3 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -71,7 +71,7 @@ export -f dge_fastqc
dge_cutadapt(){
-export Ill_ADAPTERS=/projects/bioinfo/common/illumina_universal_index.fasta
+export Ill_ADAPTERS=/projects/bioinfo/common/cutadapt_patterns.fasta
for fastqFile in $* ; do
# DEBUG fastqFile=/projects/bioinfo/holger/projects/helin/mouse/treps_pooled/mouse_liver_polar_stage1_rep4.fastq.gz
@@ -288,7 +288,7 @@ tmpDbDir=$(mktemp -d)
cp -r . $tmpDbDir
## todo remove this hack
-genome=$(echo $gtfFile | cut -f7 -d'/'); echo "genome is $genome"
+genome=$(echo $gtfFile | cut -f8 -d'/' | tr '[:upper:]' '[:lower:]'); echo "genome is $genome"
## make sure to use temp-r to avoid file locking problems
export R_LIBS=/tmp/r_index
--
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