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 https://main.g2.bx.psu.edu/root/display_as?id=11632524&display_app=ucsc&authz_method=display_at: 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: http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19 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 +

[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 ccanch...@gmail.com ___ The Galaxy User list should be used for the discussion of Galaxy analysi