added feature counts to star workflow

dge_workflow/dge_utils.sh

@@ -19,6 +19,10 @@ export PATH=/home/brandl/bin/deepTools/bin:$PATH
 export PATH=/projects/bioinfo/holger/bin/FastQC_0.11.2:$PATH
 export PATH=/projects/bioinfo/holger/bin/bedtools-2.23.0/bin/:$PATH
 export PATH=/home/brandl/bin/spinr:$PATH
+export PATH=/home/brandl/bin/subread-1.4.6-p3-Linux-x86_64/bin:$PATH
+
+
+
 # which tophat;  which bowtie2; which cuffdiff
 
 

dge_workflow/star_align.sh

@@ -92,9 +92,18 @@ done
 
 wait4jobs .tophatjobs
 
+dge_bam_correlate . &
+
+
+## estimate expresssion with http://bioinf.wehi.edu.au/featureCounts/
+##Summarize multiple datasets at the same time:
+#featureCounts -t exon -g gene_id -a annotation.gtf -o counts.txt library1.bam library2.bam library3.bam
+
+#bamFile=control_3.bam
+#featureCounts -t exon -g gene_id -a ${gtfFile} -o feature_counts.txt ${bamFile} -T 5
+mysub "${project}__feature_counts" "featureCounts -t exon -g gene_id -a ${gtfFile} -o gene_counts.txt $(ls *bam) -T 5" | blockScript
 
 
-dge_bam_correlate . &
 
 ## create tophat mapping report
 ## todo adjust report to STAR