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Old 02-02-2010, 08:34 AM   #1
Junior Member
Location: Newark, New Jersey

Join Date: Jan 2010
Posts: 6
Default Analysing the Bowtie output.

Hi all,

I am right now working with bowtie..trying to map the RNA seq.
I got the SAM output and now i want to see the mapping occuring on the genome. Is there any tool which does the annotation after getting the output file from Bowtie.

From the manual i was able to understand what each column mean but i am actually looking for how to proceed further.

Thanks in Advance

anusha is offline   Reply With Quote
Old 02-03-2010, 06:40 AM   #2
Location: Kansas City

Join Date: Oct 2009
Posts: 88

Hi Anu,

I'm right there with you. I'm mapping Solexa sequencing data, and would like to be able to do the same, compare the aligned regions to a set of annotated regions and see what was present in the alignment.
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Old 02-03-2010, 05:53 PM   #3
Location: Philadelphia

Join Date: Jul 2009
Posts: 16

Hi Anu,
I used
1. IGV ( to visualize the bam file. It's a java program, you have to download it to your computer.

2. ucsc genome browser supports bam file. Please read:
lifeng.tian is offline   Reply With Quote

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