Thanks Jen,

Another problem is with reference-guided assembly. When I produce Cufflinks assembled transcripts files and Cuffcompare combined transcrips file on my own data, it works fine with Galaxy. However, files cannot be visualized in UCSC browser-command "display at UCSC main" produces internal server error. When I try to upload them manually, I receive message "File xxx.gtf' - GFF/GTF group NM_005638 on chrX+, this line is on chrY+, all group members must be on same seq and strand "
Any idea on what does it mean and how to fix it?

Aleks




Quoting Jennifer Jackson <j...@bx.psu.edu>:

Hello Aleks,

Thank you for bring these hg18/hg19 problem to our attention - it was introduced during an edit last week and has now been corrected.

The good news is that results are obtained with either - the issue with overlap may be with the Visualization tool itself. When very "zoomed out", the overlap regions can vanish if small enough (we will be correcting/normalizing for this). However, the data is there if you just zoom in, as in the attached screenshot.

Hopefully this helps!

Best,

Jen
Galaxy team

On 6/24/11 6:19 AM, Aleks Schein wrote:
Dear all,

I tried to follow the Cufflinks tutorial created by Jeremy. The problems
start with first "visualization" step. The is no overlapping at all
between Cufflinks transcripts and RefSeq Chr19 reference, provided on
the tutorial page. Was that the goal, or transcripts should overlap and
something did not work? By the way, mapping for cufflinks was done to
hg19, but reference annotation is provided at hg18. Maybe, this is the
problem?

Aleks



Quoting Robert Curtis Hendrickson <curt...@uab.edu>:

Jen,

We are running into the same problem on our local install of galaxy.
We're running Cufflinks v.1.0.1, on a BAM file (accepted_reads) from
TopHat run on mm9 based RNAseq data (paired-end 25mer), and pulled
down the changes made to galaxy last month to support the 1.0.1
version of Cufflinks.

We (think) we have mm9 indexes locally installed. We can successfully
run get_genomic_sequence on mm9 .BED's....

Turning off bias correction made no difference.

We also tried rolling back to Cufflinks v0.9.1 (including the Galaxy
patch), and got the same error

An error occurred running this job: cufflinks v0.9.1
cufflinks -q --no-update-check -I 500000 -F 0.000100 -j 0.000100 -p 4 -N
Error running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf'

An error occurred running this job: cufflinks v1.0.1
cufflinks -q --no-update-check -I 500000 -F 0.000100 -j 0.000100 -p 4 -N
Error running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf'

I can provide a link to the history on our server that you should
(theoretically) be able to access.

Regards,
Curtis



-----Original Message-----
From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-
boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson
Sent: Friday, June 10, 2011 3:58 PM
To: David Robinson
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Error running cufflinks on Galaxy

Hello David,

Cufflinks requires locally cached data to perform the Bias Correction
function.

Without seeing any sample data, a quick guess is that changing the
option "Tool: Cufflinks -> Perform Bias Correction:" from yes to no in
that workflow step will probably correct the problem.

Another option is to set the dbkey value in the initial input FASTQ file
to be a native database (if possible).

Hopefully this helps, but if does not correct the problem, please share
a history link with data that demonstrates the problem and I can take
closer look (emailing link to me directly, to maintain data privacy,
would be fine).

Jen
Galaxy team

On 6/8/11 12:07 PM, David Robinson wrote:
Hello,

When I attempt to run cufflinks based on .sam output from bowtie I get
an error:

An error occurred running this job: /cufflinks v1.0.1
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p
8 -b
/galaxy/data/hg19/sam_index/hg19.fa
Error running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf'

/What can I do to get around this problem and run cufflinks?

My workflow is on http://main.g2.bx.psu.edu and can be found here
(I ran
it using a .fastq file):

http://main.g2.bx.psu.edu/u/dgrtwo/w/cufflinks-workflow-imported-from-
uploaded-file

Thanks in advance for your help!

-David


************************************************

David Robinson
Graduate Student
Lewis-Sigler Institute for Integrative Genomics
Carl Icahn Laboratory
Princeton University
646-620-6630

************************************************



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--
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http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
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using "reply all" in your mail client. For discussion of
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use the Galaxy Development list:

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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/




--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/



___________________________________________________________
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Galaxy analysis and other features on the public server
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