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 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 wrote: I was wondering if Galaxy has any work flow for

[galaxy-user] Exome seq work flow

I was wondering if Galaxy has any work flow for calling mutations in Exome seq and then annotating. Alignment can be done by BWA. Thanks Mathew ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features

[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 serve

[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 shou

Re: [galaxy-user] Adding a custom genome for using MACS in Galaxy

for bacterial genes under any other tool in galaxy. Thanks Mathew From: Jennifer Jackson To: Mathew Bunj Cc: "galaxy-user@lists.bx.psu.edu" Sent: Monday, September 10, 2012 11:32 AM Subject: Re: [galaxy-user] Adding a custom genome for using MACS

[galaxy-user] Adding a custom genome for using MACS in Galaxy

I have  a chipseq data which ha sbeen alined against bacterial genome. I am trying to figure out how I can use peak calling MACS in Galaxy main server. Do I need to use the bactaerial genome (in genome option of data uplaod) in uplaoding the data. Could some one diect me if I can add my own cust

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 To: Mathew Bunj Cc: shamsher jagat ; Jennifer Jackson ; "galaxy-user@lists.bx.psu.edu" Sent: Thursday, August 16, 2012 3:12 PM Subject: Re: [galaxy-

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 To: shamsher jagat Cc: galaxy-user@lists.bx.psu.edu Sent: Thursday, A

[galaxy-user] Question about Unified genotyper

I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are failing.   1. With Unified genotyper it give me message saying Sequences are not currently available for specified build. I have hg19 related data and using default  settings  (pick up hg_g1k_v37 no

[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 ne