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Old 04-24-2012, 09:51 AM   #1
oxydeepu
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Default 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
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Old 04-24-2012, 03:01 PM   #2
sdriscoll
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the map file?
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Old 04-24-2012, 09:44 PM   #3
oxydeepu
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Sorry for incomplete question. I meant from the bowtie output file.

Deepak
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Old 04-24-2012, 11:19 PM   #4
sdriscoll
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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.
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Old 04-24-2012, 11:43 PM   #5
oxydeepu
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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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