fix: htseq-count sort is by alignment not name

meono · Jul 27, 2016 · b216225 · b216225
1 parent 6d85884
commit b216225
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/iLoop_RNAseq_pipeline/master_qsub.py b/iLoop_RNAseq_pipeline/master_qsub.py
@@ -178,7 +178,7 @@ def mapandlink_jobs(project_path, sample, reads, defaults, ref, jobs, ppn='8', w
 
     if any(job for job in jobs if job in ['htseq-count', 'edgeR', 'DESeq']):
         logger.info('Using htseq options: {}'.format(defaults['htseq_options']))
-        jobstr += ['echo "htseq"\nhtseq-count {} -f bam {} {} -o {} > {}'.format(defaults['htseq_options'],
+        jobstr += ['echo "htseq"\nhtseq-count {} -f bam -r pos {} {} -o {} > {}'.format(defaults['htseq_options'],
                                                                                  (os.path.abspath(
                                                                                      os.path.join(project_path, sample,
                                                                                                   'accepted_hits.sorted.bam'))),