Speaking of which, could a Galaxy developer look at adding these
changes, please?
https://bitbucket.org/galaxy/galaxy-central/issue/447/new-tools-to-de-interlace-fastq-mate-pair
Thanks,
Florent
On 23/03/11 12:02, Jeremy Goecks wrote:
Alternatively, we welcome community contributions to the
Date: Wed, 18 May 2011 10:31:21 +1000
From: Florent Angly florent.an...@gmail.com
To: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu
Hi all,
I was wondering if there is a way to put conditional statements in a
Galaxy workflow.
This would be useful, for example, in the case
Hi Haluk,
By filtering, you mean removing reads? trimming their ends? or masking
some of their bases?
There are 3 tools under Generic FASTQ manipulation that may help you:
Filter FASTQ reads by quality score and length
FASTQ Quality Trimmer by sliding window
FASTQ Masker by quality
for removing bases.
After your reply, I got suspicious. Am I trying to do something wrong
in theory?
Thanks in advance.
On Sun, Jul 31, 2011 at 6:07 AM, Florent Angly
florent.an...@gmail.com mailto:florent.an...@gmail.com wrote:
Hi Haluk,
By filtering, you mean removing reads? trimming
For read simulation, you may also want to give Grinder a try. I made a
Galaxy wrapper for it (see in the toolshed: http://toolshed.g2.bx.psu.edu/)
Florent
On 20/09/11 18:46, Kevin Lam wrote:
Hi Daniel,
You would have multiple names for each sequence and that would be
quite hard to display. I
additional problems.
Thanks for finding this!
Greg Von Kuster
On Oct 4, 2011, at 2:53 AM, Florent Angly wrote:
Hi all,
I tried the latest stable version of Galaxy:
http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to how
to use the new tool shed including how
I have had the chance to try the patch on several datasets and it looks
good :)
I reiterate my suggestion to pull the patch in galaxy-central.
Best,
Florent
On 05/10/11 18:28, Florent Angly wrote:
Hi,
I have found some issue with the way FASTQ read description is handled
by Galaxy
Peter and Daniel, thanks for the comments.
On 19/10/11 23:49, Peter Cock wrote:
On Wed, Oct 19, 2011 at 2:31 PM, Daniel Blankenbergd...@bx.psu.edu wrote:
Hi Florent,
Sorry for the delay. I did try the patch out shortly after you contributed
it, but it caused the functional to fail. I was
Hi Joanna,
During trimming, some of the reads may be removed from your dataset.
Depending on what you need to do, you may or may not want to discard
reads that don't have a mate mate anymore. If so, you might consider
using the FASTQ de-interlacer and interlacer tools.
Florent
On 26/10/11
On 19/10/11 23:31, Daniel Blankenberg wrote:
Sorry for the delay. I did try the patch out shortly after you
contributed it, but it caused the functional to fail. I was able to
fix the issue and allow the existing tests to start passing, but I've
been bogged down lately and haven't been
Hi,
I just tried to upload a new version of the Grinder Galaxy wrapper to
the Galaxy ToolShed and am encountering difficulties that I did have in
previous versions.
When I upload my .tar.gz file, the upload is aborted and I get the error:
'GalaxyWebUITransaction' object has no attribute
instance with no problems, so I believe your grinder
repository is now in a good state. Thanks very much for reporting this issue.
Greg Von Kuster
On Jan 17, 2012, at 8:43 PM, Florent Angly wrote:
Hi,
I just tried to upload a new version of the Grinder Galaxy wrapper to the
Galaxy ToolShed
12 matches
Mail list logo
