Analysing the Bowtie output.

[anusha]

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

Anu

[DrD2009]

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.

[lifeng.tian]

Hi Anu,
I used
1. IGV (http://www.broadinstitute.org/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: http://genome.ucsc.edu/goldenPath/help/bam.html