Hello Miro,
It sounds like perhaps the datatype is not being assigned correctly,
which may mean that they quality scores are not scaled properly. To
double check both, see the instructions in our wiki here:
http://wiki.galaxyproject.org/Support#Dataset_special_cases
If you still need help aft
Hi Michael,
Thanks for reporting this, sounds like an older, incorrect, config
file is in place. And this can be fixed.
I will be going into the genomes area and re-verifying current
builds and other built-in data/indexes shortly.
Thanks!
Jen
G
Hello Kumar,
The NGS queue has been down for several days now. We expect this to be
up soon. This is related to the upgrades on the public Main server, as
noted in the top banner. Leaving jobs queued will ensure that they are
processed when this queue opens again.
The simplest alternatives f
Hi Delong,
If you are mapping against a large reference genome and your datasets
are large, 8G of memory may simply not be enough, even with omitting
this paramater. Also, if you have set other TopHat parameters to be
sensitive, then those can also be contributing to memory usage.
Splitting t
Hi -
Pls see below
On 8/27/13 6:36 AM, Delong, Zhou wrote:
Hello,
I have run several analysis with Tophat 2 on my local instance of
galaxy and I get this error for all of them..
segment-based junction search failed with err = 1 or -9
Here is an example of full error report:
Error in tophat
Regarding (2), have you installed bowtie and tophat on your Mac Pro?
Galaxy does not currently automatically install all of the software
needed to run tools (we are working on this through the toolshed, but
at the moment it is a manual process).
Dependencies of various tools included in the distri
Hello,
You will need to provide a GTF or GFF3 file to Cuffdiff - this is what
the tool uses as a reference base to build gene, transcript, and if
provided in the annotation attributes, transcript start site and protein
groupings to perform the differential analysis.
More details can be found her
Hello Lilach,
The public Main Galaxy server is very busy right now, but I do see your
account in the queue (as I have since you first sent this email). We
expect the processing time to improve soon. Meanwhile, the best strategy
is to leave queued job alone and not stop/restart or they will mov
Hello Dipanjana,
I am not sure if you mean that the job is actually running (yellow) or
has been waiting in the queue (grey) during this time period (or some
combination), but I can let you know that both processes can vary in the
length of time they take to execute.
A job in the queue (grey
Tophat should be used when mapping reads to the genome, not the transcriptome.
Because you're mapping your reads to the transcriptome assembled via Trinity,
Bowtie or BWA are good choices.
This also changes your downstream analyses, because Cufflinks does not work
well on reads mapped to the tr
Hello Humberto,
Are you using the public Main Galaxy instance at
http://main.g2.bx.psu.edu (http://usegalaxy.org)? If so, and a re-run of
the job still fails, please submit a bug report so that we can provide
feedback.
http://wiki.galaxyproject.org/Support#Reporting_tool_errors
There was a s
Hi Wei,
Have a look at RNASeQC which provides more than what you specified here.
(https://confluence.broadinstitute.org/display/CGATools/RNA-SeQC)
This generates a detailed report with all relevant metrics on your RNA data.. I
think, integrating this - a java based tool - into Galaxy should res
It isn't normal, but this can happen during periods of extremely high load like
we're currently experiencing. If you leave your jobs in the queue, they'll
execute as soon as possible - don't cancel or restart your jobs as this will
only move them to the back of the queue and delay completion.
Hello Xiefan,
On 9/10/12 12:16 PM, Xiefan Fang wrote:
Dear galaxy users,
I aligned my RNA-seq data by using Tophat in galaxy. It generated
some “Tophat deletions”, “Tophat insertions” and “Tophat splice
junctions” results. These are all BED files. Does anyone know how to
use/analyze thes
Hello Irene,
The file is described in the TopHat manual:
http://tophat.cbcb.umd.edu/manual.html#output
Along with the insertion files, deletions describes variation between
the query and the reference genome at the base level (nucleotide). It
does not describe whole transcripts or genes.
How
Hello Irene,
Please see:
http://wiki.g2.bx.psu.edu/Learn/Datatypes#Learn.2BAC8-Datatypes.Bed
The BED data format was created by UCSC:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1
The TopHat manual also links to the UCSC specification:
http://tophat.cbcb.umd.edu/manual.html (scroll to "TopH
Hi,
I actually fixed it. I changed the wrapper in the line 105 from:
cmd_index = 'bowtie-build %s -f %s %s' % ( space, options.own_file,
index_path )
to
cmd_index = 'bowtie2-build %s -f %s %s' % ( space, options.own_file,
index_path )
Luciano
On Tue, Jun 19, 2012 at 3:03 PM, Luciano
Hi Jiwen,
Please submit this error using the green bug icon associated with the dataset
and we can check to see if this is related to the other issues discussed
earlier today.
Thank you,
Jen
Galaxy Team
On Apr 27, 2012, at 3:18 PM, 杨继文 wrote:
> Hi all,
> I got the following error infomation
> Jeremy, do you have a workflow to estimate what percent of the reads
> are mapping to unknown expressed regions?
Here's a simple approach assuming mapped reads are in BAM format:
BAM --> SAM
SAM --> Interval
Intersect reads as interval with known annotation not allowing for any overlap.
Bes
On Wed, Apr 18, 2012 at 8:37 AM, Jeremy Goecks wrote:
> I am wondering if these "non-coding reads" will be included when cufflinks
> calculates transcript/gene expression.
>
>
> Reads will only be included if they map to assembled/known transcripts.
Well it depends what transcript annotation file
> I am wondering if these "non-coding reads" will be included when cufflinks
> calculates transcript/gene expression.
Reads will only be included if they map to assembled/known transcripts.
> And another question is: how to know the number of reads mapped to a certain
> exon?
This isn't pos
Jiwen, I wonder if you are thinking about the situation where you
could be discarding reads that are to short after trimming?. In that
case you could be getting the two files out of sync. If this is the
case, I think you do need to join the files first, do the trimming and
then take them apart agai
Hello Jiwen,
No, you do not need to join the files for the quality processing.
Hopefully this helps!
Best,
Jen
Galaxy team
On 4/9/12 9:14 AM, 杨继文 wrote:
Hi all,
I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate
files. Before mapping, I need to trim the reads.
My questions i
Hi,
Thanks for the reply, sorry about the multiple posts - it kept getting bounced
so I resubmitted the question. We seem to be having real problems with our
local install so I'll add it to the list...!
Cheers
David
On 14 Mar 2012, at 18:10, Jennifer Jackson wrote:
> Hi David,
>
> You ques
Hi David,
You question has posted to the list now and we will be getting back to
you. It didn't post immediately due to some mail mailman server issues here.
This looks like a problem that came up on a local instance. Because of
that, I am going to send this over to the galaxy-...@bx.psu.edu
Hi JIwen,
As the seqanswers thread shows, there is some debate about this. One of
the last posts there makes the most sense - where "fragment length" is
defined as the total genome bases covered by the aligned paired
sequences: tip of 5' start, through the gap, to the very 3' tail end and
whe
Hello Jiwen,
The tool "NGS: Picard (beta) -> SAM/BAM Alignment Summary Metrics" gives
a nice set of statistics for paired end data.
Hopefully this helps,
Best,
Jen
Galaxy team
On 3/7/12 12:35 AM, 杨继文 wrote:
Dear all,
This might be a silly question, but I couldn't figure it out by myself
:-
Hi Jiwen,
This is a subject that has me very confused too. This thread at
seqanswer didn't help much either:
http://seqanswers.com/forums/showthread.php?t=8730
But it does have some good comments on the subject.
I did try using the two possible options I can think of:
fragment length - pair end
Hi Genaro,
For reference, these are the tool version recommended for use with local
installs:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
for Bowtie, the supported version is 0.12.7
for Tophat, the supported versions are 1.3.3-1.4.0
for Cufflinks/merge/diff, the supported version
Genaro,
> My question is which are the best/appropiate TOPHAT and CUFFDIFF versions?
Galaxy wrapper versions do not match tool versions. The tag 'requirements' will
eventually be used to specify versions, but this work is not yet complete.
You should use Tophat v1.4.0 or 1.4.1 and Cufflinks v1.
You're correct Jack. I've modified the Tophat wrapper to remove this
restriction; the change will make its way to our public server soon.
Best,
J.
On Feb 8, 2012, at 1:27 PM, Jack Colicchio wrote:
> In the new version of tophat they allow for over 3 mismatches in the initial
> alignment, howev
Hello Jiwen,
It is possible to view both the TopHat and Cufflinks output together in
Trackster. Are you doing this?
Are you seeing that reads/transcripts are spanning the splice regions
(align to one side, span the gap, then align to the other side)? This is
what would be expected for RNA-se
On Dec 14, 2011, at 11:19 AM, Magdalena Strzelecka wrote:
> Hi,
>
> I have submitted some jobs to Tophat, but they have not started since
> yesterday (Dec 13th); i.e they were in a queue for >12 hrs. I have
> re-submitted everything again (2 jobs), but the same situation is happening.
> Is th
Hi Alessia,
Shamsher is correct, Trackster is a great choice for viewing data.
The Galaxy Track Browser (aka Trackster) has several new features and
more coming up in the next few weeks at the Main instance. This tutorial
covers a basic RNA-seq analysis that includes visualization:
http://mai
Ues IGV or Galaxy tracker.
On Wed, Nov 9, 2011 at 9:37 AM, Alessia D wrote:
> How do people on this mailing list usually visualize Tophat and/or
> Cufflinks results (eg. tracks on UCSC browser)?
>
> I have only this once before, and I started with a .wig file that I
> uploaded to the genome br
Thanks Jen for your answer
Zohra
> Date: Tue, 11 Oct 2011 13:01:37 -0400
> From: j...@bx.psu.edu
> To: saci...@live.fr
> CC: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] tophat error
>
> Hi Zohra,
>
> One more bit of help: in the past our team has notice
Hi Zohra,
One more bit of help: in the past our team has noticed that Color Space
files from NCBI's SRA database have a "placeholder" adapter base quality
score added in (for an unknown reason).
If you choose to use Galaxy, when passing the file through the FASTQ
Groomer tool (with input and
Hello Zohra,
For command line (not Galaxy) use of this tool, questions would be best
directed to the tool authors at tophat.cuffli...@gmail.com. That said,
there appears to be a mismatch between the quality scores in your fastq
file and what was expected (integer, linked to the -C option).
S
Hi Rich,
Are you using a local instance or the main public instance at
http://usegalaxy.org?
There was a bug fix to this tool on the public instance right around the
time this error was reported. Please try the job again. If it fails, it
may be that the files are too large, although an error
Hello Luciano,
Here are is the core wiki link to help with NGS tools (including
SamTools) set up and installation.
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
For next time, the galaxy-...@bx.psu.edu mailing list would be the best
place to send new questions or even follow-up questio
Hi Song,
We have alpha support for Tophat v1.3.0 and it appears to work fine with
Galaxy's Tophat wrappers. We'll upgrade and start full testing near term.
For now, when running in a local instances, we do encourage users to try
it and see if it meets their needs. Perhaps try with an uncompre
Hello Song Li,
The file extension seems to be a mismatch.
file.gz <- "gzip" utility
Exploring the use of gunzip or zcat are options to restore a "file.z".
Hopefully this helps,
Jen
Galaxy team
On 7/19/11 11:52 AM, Song Li wrote:
Hello everyone,
I was trying to run tophat in a local version
Hi David,
Will be updated to 1.2.0 when main is next updated (soon).
Once implemented, feedback about how the update functions would be welcomed,
Best,
Jen
On 3/14/11 1:14 PM, David Matthews wrote:
Hi,
Just wondering when the tophat portion of Galaxy will be updated? Its currently
version 1
43 matches
Mail list logo
