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-   -   Bowtie alignment distribution (http://seqanswers.com/forums/showthread.php?t=19477)

oxydeepu 04-24-2012 09:51 AM

Bowtie alignment distribution
 
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 04-24-2012 03:01 PM

the map file?

oxydeepu 04-24-2012 09:44 PM

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

Deepak

sdriscoll 04-24-2012 11:19 PM

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 04-24-2012 11:43 PM

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


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