Re: [galaxy-user] SNP finding

2013-11-11 Thread Nate Coraor
Hi Mark, This error is not tool related. Could you click the “bug” icon to send us an error report? —nate On Nov 11, 2013, at 8:33 AM, Mark Lindsay wrote: > Dear Galaxy Users > > I wondered if anybody is having the same problem. > > I am trying to run CuffDiff using the latest version of G

Re: [galaxy-user] SNP finding

2013-11-11 Thread Jennifer Jackson
Hello Xiefan, This page has a simple breakdown of how to call variants within Galaxy. This is brand new, so full annotation/video is pending, but it should still be straightforward to see how the data is prepped and which tools are used. https://usegalaxy.org/u/galaxyproject/p/galaxy-101-ngs-

Re: [galaxy-user] SNP finding

2013-11-11 Thread Mark Lindsay
Dear Galaxy UsersI wondered if anybody is having the same problem.I am trying to run CuffDiff using the latest version of GenCode18 and keep getting the following error message.Is there a problem with the network or is it me?Best wishesMark___

[galaxy-user] SNP finding

2012-10-21 Thread Xiefan Fang
Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads p

[galaxy-user] SNP finding

2012-10-21 Thread Xiefan Fang
Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads p