Unmapped reads from tophat

20 Nov
2012
20 Nov
'12
5:21 a.m.
Hello, Is there a way to get unmapped reads from tophat? The accepted hits bam output only contains mapped reads (confirmed with flagstat) Am I overlooking an option or tool? Thanks Kevin

20 Nov
20 Nov
9:04 a.m.
On Nov 20, 2012, at 11:21 AM, Kevin Y wrote:
Hello, Is there a way to get unmapped reads from tophat?
Only the very latest tophat version 1.4.1 IIRC (and maybe tophat2 from the beginning) save unmapped reads into a fastq.gz file output, and its not an option. I don't think the galaxy output puts this into your history yet. best, ido
4462
Age (days ago)
4462
Last active (days ago)
1 comments
2 participants
participants (2)
-
Ido Tamir
-
Kevin Y