Daniel:
To get a good idea on how Galaxy handles so called interval operations take a look at http://usegalaxy.org/galaxy101. The answer to your question depends on what you would like to do. Are interested in obtaining the read coverage for a set of genes or simply identifying a set of reads mapping to a set of genes?
Thanks,
anton
On Apr 11, 2011, at 11:17 AM, Daniel Elleder wrote:
Hi,
I have reads from Illumina paired-end run mapped against reference genome using Bowtie. Is there a Galaxy tool which would allow me to extract gene names from the mapped chromosomal regions? In this case I have cat genome, example of the output row is bellow.
Thanks for anymhelp, Daniel
HWUSI-EAS610_110227_00028:5:1:7767:999#0 99 chrE2 27900093 255 82M = 27900139 128 NACCTGTTATGTACTAAGAAGCTTATTCTCCCANNNNNNCTNNNNNNNNNCATATGTNGNGNNNNNNNNNNNNNNNNNNNAA ################################################################################## XA:i:2 MD:Z:0A17T14T0G0C0T0G0A2C0A0T0C0A0A0A0G0G7G1T1A0C0C0C0C0T0T0A0G0T0G0C0C0C0G0T0G0A0T2 NM:i:38
Daniel Elleder, Ph.D. Postdoctoral fellow Center for Infectious Disease Dynamics Pennsylvania State University 613 Mueller Laboratory University Park, PA 16802 tel: (814) 867-2122
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