Bowtie ouput in Tophat

unidodo · 03-29-2011, 10:49 AM

Just wondering if anyone knows how to get Bowtie output such as % of mapped unique reads when we run Tophat?

Thanks in advance.

ttnguyen · 03-29-2011, 12:22 PM

I don't think we can get Bowtie mapping summary if we use Tophat since Tophat may split your reads and employes Bowtie at several steps. I think you might find that information by looking at accepted_hits.bam

unidodo · 03-30-2011, 01:13 PM

Finally, I found such info in the files under the tophat output folder.

There are two files. One is the genome, another is the junction sequences.

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03-29-2011, 10:49 AM	#1
unidodo Junior Member Location: USA Join Date: Jul 2010 Posts: 8	Bowtie ouput in Tophat Just wondering if anyone knows how to get Bowtie output such as % of mapped unique reads when we run Tophat? Thanks in advance.

03-30-2011, 01:13 PM	#3
unidodo Junior Member Location: USA Join Date: Jul 2010 Posts: 8	Finally, I found such info in the files under the tophat output folder. There are two files. One is the genome, another is the junction sequences. Last edited by unidodo; 03-30-2011 at 01:24 PM.

03-29-2011, 12:22 PM	#2
ttnguyen Member Location: Ireland Join Date: Mar 2010 Posts: 41	I don't think we can get Bowtie mapping summary if we use Tophat since Tophat may split your reads and employes Bowtie at several steps. I think you might find that information by looking at accepted_hits.bam