Closed Kurt-Hetrick closed 4 years ago
got some bam files that had a mixture of paired end and single end reads...so yeah, will have to do something about that...might just have to do some hack job and do things somewhat manually for those couple of files.
actually, i was able to implement this into the pipeline. if FASTQ_2 is null then run a single end cmd for bwa, if not, then run paired end.
got some bam files that had a mixture of paired end and single end reads...so yeah, will have to do something about that...might just have to do some hack job and do things somewhat manually for those couple of files.