Bowtie alignment distribution

[oxydeepu]

hi all,

I have aligned my RNA-Seq reads to the reference genome using bowtie. Now i want to know where the reads are getting aligned from the map file - like is it coming from repetitive element or exon, etc.
Please help. Thank you in advance.
Deepak

[sdriscoll]

the map file?

[oxydeepu]

Sorry for incomplete question. I meant from the bowtie output file.

Deepak

[sdriscoll]

So the next step would be to use a tool like Cufflinks to quantify expression of genes in terms of some annotation - typically a GTF file from ensemble or UCSC's table browser. That and make a bedGraph of your alignments so you can view them in the UCSC genome browser.

[oxydeepu]

Thank you.

Is there any other way we can figure out from the alignment output whether it is coming from an exonic region or repeat region.

Cheers
Deepak