new adapater set for trimming

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