[galaxy-user] FastX Clipper on FastQ data

Hi List, I have a couple of miRNA-Seq files (Illumina GAIIx, 29nt read length). These reads contain differing amounts of 3' adapter sequences and therefore map really badly to the human genome (with eland v2). Therefore, I'd like to use the FastX clipper tool, which states that This tool

Re: [galaxy-user] FASTQ type change

On Thu, Feb 10, 2011 at 6:42 PM, Peter wrote: On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor wrote: Sounds like this should be added into the main release. It would save a lot of time/disk space instead of using Groomer. I agree. Maybe Dan can take care of it - I don't have bowtie setup

Re: [galaxy-user] Upload via SCP?

Felix Hammer wrote: Hi, is it possible to use SCP to upload files instead of FTP? Hi Felix, At this time, no. --nate thxbye, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

[galaxy-user] Importing GTF into Galaxy

Hi, I have been trying to get reference data from the ucsc browser into Galaxy, but when I try to get the rat genome in gtf format, I only get files halfway through chomosome 10. This happens with both of the available builds for the rat. I am guessing this is a problem with the UCSC files

[galaxy-user] GeneTrack Server Error

Hi, I am trying to view Converted Interval Data in GeneTrack, but all I get is Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) thx, Felix ___ The Galaxy User list should be

Re: [galaxy-user] FASTQ type change

Hi Stephen and Peter, This change is definitely possible, and because the SAM format specifies that its quality scores are phred scaled and ASCII offset of 33 (regardless of provided input) it shouldn't cause complications downstream. We'll add this to our todo list. I created a ticket: