From 6cd1c5e386cc3b66d851c43afea12c9ff621aab5 Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 16 Jun 2015 14:07:07 +0200
Subject: [PATCH] added feature counts to star workflow
---
dge_workflow/dge_utils.sh | 4 ++++
dge_workflow/star_align.sh | 11 ++++++++++-
2 files changed, 14 insertions(+), 1 deletion(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index 9cc7225..516d609 100755
--- a/dge_workflow/dge_utils.sh
+++ b/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
diff --git a/dge_workflow/star_align.sh b/dge_workflow/star_align.sh
index ce937ad..927db03 100755
--- a/dge_workflow/star_align.sh
+++ b/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
--
GitLab