[galaxy-user] To post to list

2011-12-08 Thread Rose Iszati bte. Ismet
rose_is...@yahoo.com ___ 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

[galaxy-user] GI error/shift in the output of megablast ?

2011-12-08 Thread Sandrine Hughes
Dear all, I have a trouble with the Megablast program available in NGS Mapping and I hope that you can help. Indeed, I think that there might be a problem with the table given in output, and notably a shift between the GI numbers and the parameters associated. Here are the details: I. First,

[galaxy-user] cufflinks-status-FAIL

2011-12-08 Thread dongdong zhaoweiming
Hi,   I used the cufflinks to assemble my SAM file, but the results showed some CUFF's status in not OK,it's FAIL, so that means these CUFF's corresponding sequence  could not used or else mean? Thanks a lot!   Reards weimin zhao___ The

Re: [galaxy-user] cufflinks-status-FAIL

2011-12-08 Thread Jennifer Jackson
Hello Weimin, The majority of issues user's encounter with RNA-seq tools is related to the inputs, so troubleshooting format is the first step. Please see the section Example: unexpected results with RNA-seq analysis tools here:

[galaxy-user] January 2012 Galaxy Events: Dec 15 Deadline for Czech Republic Workshop

2011-12-08 Thread Dave Clements
Hello all, The January Events http://wiki.g2.bx.psu.edu/Events email is going out a little early this month, mainly because of a *December 15 deadline for the Galaxy Developer Workshop in the Czech Republichttp://evomics.org/workshops/galaxy-developer-workshop/ *. There are Galaxy-related events

[galaxy-user] Galaxy Bowtie alignment stats report

2011-12-08 Thread Eric Guo
Hello, Does anyone know how to get alignment stats from Bowtie on Galaxy? I would like to know what percentage of total reads from my dataset is aligned. I know if you run Bowtie using the command line, it gives you the report. However, I could not find percent alignment on Galaxy. Thanks