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 > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
