Re: [galaxy-user] Data sources don't load in Firefox

2013-09-12 Thread Jennifer Jackson
Hi Carrie, We are aware of this new issue with the Firefox 23.0.1 update. Using an alternate browser is recommended to avoid the problem with direct https-http connections, as several of Galaxy's Get Data tools/sources are impacted. Our team is reviewing solutions at a priority. Hopefully

Re: [galaxy-user] (no subject)

2013-09-12 Thread Jennifer Jackson
Hi Maria, This message indicates that an error occurred on the cluster node processing the job. Normally these are not linked to inputs or tools and the general solution is to re-run the job. Please give this a try today - it is possible the error was linked to recent transient server issues.

Re: [galaxy-user] extension of read length

2013-09-12 Thread Jennifer Jackson
Hi Tobias, In general, you can use *'**NGS: Picard (beta) - SAM to FASTQ'* to extract sequences (convert BAM SAM first), but this tool does not add in extra sequence based off the reference genome (or pad the associated quality scores, etc.). I don't know of a Galaxy wrapped tool that does

[galaxy-user] display at ucsc error

2013-09-12 Thread lilach noy
Hey there, I am trying to add a custom track of a bed file through Galaxy and i keep getting this error: - Error line 325149 of chrM_rCRS not a recognized sequence (note: sequence names are

Re: [galaxy-user] display at ucsc error

2013-09-12 Thread Hiram Clawson
Please note, this sequence chrM_rCRS does not exist in the human/hg19 genome browser at UCSC. It is not a recognized sequence. There is a note about this on the gateway page: See the paragraph titled: Note on chrM --Hiram On 9/12/13 1:25 AM,

[galaxy-user] About Slice BAM tool

2013-09-12 Thread Yan He
Hi Jen and other galaxy-users, I was using Slice BAM tool on Galaxy to get the alignment overlap with the targeted intervals. After I got the output BAM file, I used flagstat to get the detailed information of the output BAM file. What I got from flagstat is as following. 13704486 + 0 in

[galaxy-user] de novo RNA-Seq workflow

2013-09-12 Thread Carlos Canchaya
Hi guys, I am looking for a de novo RNA-seq workflow that uses trinity. Any idea if there is one available? Bests, Carlos Carlos Canchaya ___ The Galaxy User list should be used for the discussion of Galaxy