Thanks for your input and patience, Holger!
Please try the new version 0.4 of the weblogo wrapper in
galaxy-central #5772 - it has additional error reporting that may help
clarify dependency or other problems and let me know how you go?
On Tue, Jul 5, 2011 at 5:49 PM, Holger Klein wrote:
> Hi Ro
Hi all,
Is there any way to find out the number of reads aligning to a transcript
rather than the FPKM calculated by Cufflinks?
I'm also interested in obtaining summary statistics for mapping analyses or
RNA-Seq data, such as % of reads aligned, % uniquely aligned, mapped to
exons, introns, etc.
Will submit to Galaxy my additions.
Thanks
Vasu
--- On Wed, 7/6/11, Jeremy Goecks wrote:
From: Jeremy Goecks
Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks
To: "vasu punj"
Cc: "GavinOliver" , "David Matthews"
, "galaxy-user"
Date: Wednesday, July 6, 2011, 10:08 AM
Kurinji,
> 1. when I look at my differentially expressed transcripts file (generated
> using ensembl hg19 as a reference with chr added on to obtain results with
> ensembl gene names) and search for specific genes that I am interested in I
> can not find them in my cuffdiff output file - even t
Looks like a bowtie error.
The first chunk memory size can be increased on the command line with
--chunkmbs=128
The default is 64.
I don't know if this is possible in Galaxy though.
-Original Message-
From: galaxy-user-boun...@lists.bx.psu.edu
[mailto:galaxy-user-boun...@lists.bx.psu.
Hello Agnieszka,
To confirm, you are using the public Galaxy site? If so, would you be
able to share a link to your history? Use "Options -> Share or Publish"
then email me directly to keep your data private.
Thanks!
Jen
Galaxy team
On 7/6/11 3:25 AM, A Bierzynska wrote:
Hi,
I was wonder
Aleks,
> I used Epicentre ScriptSeq strand-specific library construction protocol,
> which I assume, produces a second-strand library.
This an assumption probably worth verifying before going further. The Tophat
documentation may be helpful as well:
http://tophat.cbcb.umd.edu/manual.html
> Wh
> One question related to this If I am intrested in annotated
> genes/transcripts, what change I may have to make in command line while
> runnig Cufflinks so that it will give both unknown as well as known
> transcrpts and genes?
> Thanks
You probably want the -g/--GTF-guide parameter; from th
Hello all,
we have the UCSC genome browser mirror as well as Galaxy mirror. The
Galaxy has a feature enabling a user to display the data at UCSC genome
browser as custom tracks. I have configured the galaxy to display the data
to our UCSC browser mirror but it doesn't work properly: after the
redi
?
: deleting datasets from history
: Tue, 5 Jul 2011 19:58:45 +0300
??: Sergei Ryazansky
: galaxy-user-requ...@lists.bx.psu.edu
Hello all,
After the deleating datasets from the history panel in our Galaxy mirror
the indicator at the
Hi,
I was wondering if you could help me to understand an error which I get
when mapping using Galaxy:
An error occurred running this job: Error aligning sequence. Warning:
Exhausted best-first chunk memory for read
BIO-SEQUENCER1_0011:1:1:9519:2064#CGATGT/1 (patid 703); skipping read
Warni
On Tue, Jul 5, 2011 at 11:41 PM, Mete Civelek wrote:
> Hi All,
>
> I was wondering if there is a way to add tools to the Galaxy web portal (the
> central server, not our own instance of Galaxy). Some of the tools I would
> like to use are described on
> "http://toolshed.g2.bx.psu.edu/repository?w
Hi,
I would like to generate a random intervals file by mimicking a bed file
of interest from the mouse genome.
Does someone know how to do that?
NB: the "random intervals" tool from "Encode tools" does this but only
for human genome.
Thanks
Jerome
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