SEQanswers (
-   Bioinformatics (
-   -   Bowtie alignment distribution (

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.

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.


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.


All times are GMT -8. The time now is 07:42 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.