Hi Jennifer, I reload my data with defined format type fastqsanger and it works now. Thank you so much for your help.
Gang
On Thu, Feb 13, 2014 at 6:06 PM, Jennifer Jackson jen@bx.psu.edu wrote:
Hi Gang,
I can't comment about a PC (I use a MAC), but this shouldn't matter. If you are using a local Galaxy (http://getgalaxy.org http://usegalaxy.org/toolshed), most tools will follow the same usage rules as when implemented on the public Main Galaxy instance at http://usegalaxy.org, the Galaxy CloudMan ami, and the bulk of other public Galaxy instances, at least for common tools.
Exceptions would be if the tool(s) were specifically modified to function differently. Galaxy is open source and variations exist. The tool form of any alternate version (of a tool named the same) will likely note what modifications have been made. Plus you can always contact the other public instance hosts, if you have usage problems.
Best!
Jen Galaxy team
On 2/13/14 2:26 PM, Gang Wang wrote:
By the way, can you use detect the fastq file using trimmer by column with your PC. Thanks a lot.
Gang
On Thu, Feb 13, 2014 at 1:14 PM, Björn Grüning bjoern.gruening@gmail.comwrote:
Hi Wang,
please check if your fastq file is associated with the correct fastq format, fastqsanger probably.
Cheers, Bjoern
Hi,
I just notice that NGS FASTQ Trimmer by column can't detect the fastq file I loaded. Anyone knows why. thanks a lot.
On Fri, Jan 24, 2014 at 11:00 AM, galaxy-user-request@lists.bx.psu.edu wrote: Send galaxy-user mailing list submissions to galaxy-user@lists.bx.psu.edu
To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-user or, via email, send a message with subject or body 'help' to galaxy-user-request@lists.bx.psu.edu You can reach the person managing the list at galaxy-user-owner@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-user digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: Creating a Trackster visualisation from a reference in your history (Jeremy Goecks)
Message: 1 Date: Thu, 23 Jan 2014 15:49:44 -0500 From: Jeremy Goecks <jgoecks@email.gwu.edu> To: graham etherington (TSL) <graham.etherington@sainsbury-laboratory.ac.uk> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Creating a Trackster visualisation from a reference in your history Message-ID: <C3382F38-D243-4979-B6A7-BA13EF161EE5@email.gwu.edu> Content-Type: text/plain; charset="windows-1252" > Is it possible to create a custom build and use it to view a SAM file without adding the .len and .2bit files in to the Galaxy file system as an administrator? Yes, it definitely is. > If so, what am I doing wrong? This is a Galaxy bug which has been fixed in this commit:https://bitbucket.org/galaxy/galaxy-central/commits/117fef56513fc563dd231516...
We have a release coming up, so this fix will be included in the release and will make it to our public server soon. In the meantime, note that you can use the genome fasta file rather than the len file to create a custom build and everything should work. Thanks, J.