[galaxy-user] Can I call SNPs and Indels in Galaxy

I have  two  DNA seq files for hg18 and want identify SNPs in each file as compare dto existing database and also want to find differences (seq variations) among two samples. I was wondering if I can do that or not in Galaxy (public server)?   I know I can use liftover to convert into hg19 if

Re: [galaxy-user] copy number variation detcetion in Glaxay

Thanks Jen,   I am also intrested in this. Has any one used FreeBayes in Galaxy or out side Gaaxy to detect CNV from a ilumina sequencing data. Is their a tutorial for running this tools.   Thanks.   From: Jennifer Jackson j...@bx.psu.edu To: shamsher jagat kanwar...@gmail.com Cc:

Re: [galaxy-user] copy number variation detcetion in Glaxay

Thanks Erik, I was also not very clear about Freebayes use in CNV detection. Thanks for clarifiaction.   Mathew From: Erik Garrison erik.garri...@bc.edu To: Mathew Bunj mathewb...@yahoo.com Cc: shamsher jagat kanwar...@gmail.com; Jennifer Jackson j...@bx.psu.edu; galaxy-user@lists.bx.psu.edu

[galaxy-user] trimming illumina reads from 3' without considering quality score

Is it possible to trim certain number of bases from 3' end with taking into  consideration quality of reads. To explain it further, I want to remove 10bases from 3 ' end of all reads and keep first forty. Thanks ___ The Galaxy User list

[galaxy-user] Bisulfite seq

Do we have any tool which can be used for analyzing and QC check for bisulfite sequencing. I have FASTq files. Thanks Mathew___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

Re: [galaxy-user] Exome seq work flow

No I have not received any feedback as yet. Thanks On Friday, March 14, 2014 7:42 AM, Kristin Kernohan kristinkerno...@gmail.com wrote: Hi did anyone answer this? Id be curious to know as well thanks Kristin On Thu, Mar 13, 2014 at 10:22 PM, Mathew Bunj mathewb...@yahoo.com wrote: I