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
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