problems in transitioning from Tophat to Cuffdiff
After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy. I had this problem with histories developed before the move and histories developed after the move. I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC. I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories. Is anyone else having this problem? And found a solution? Elwood Linney
Are you reporting a bug for each failed Cuffdiff run? That's the easiest way for the Galaxy team to help you out. One thing to keep in mind is that, for now, spaces are not allowed in condition names. We'll address this problem soon. Best, J. On Oct 22, 2013, at 5:42 AM, Elwood Linney <ellinney@gmail.com> wrote:
After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy.
I had this problem with histories developed before the move and histories developed after the move.
I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC.
I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories.
Is anyone else having this problem? And found a solution?
Elwood Linney ___________________________________________________________ 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:
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Elwood, Would you please share: 1. an original history that worked (if possible) 2. the workflow you are using and let me know how you generated (did you extract it recently (last week or so)? 3. problem history There are a few known issues in here, some mitigated, one that has to do with extracted workflows from existing older histories that is Cuffdiff specific (actually, a few problems, found another last night). I want to rule those out or at least try to provide feedback. I am at a conference over next several days, so let's use galaxy-bugs as a cc whenever we communicate so nothing is left lingering, plus I know Nate was looking into some of your data. Jeremy may jump also in at any time and help - he is the author of the wrapper. So, in your *reply*, _remove galaxy-user@bx.psu.edu_ and _add galaxy-bugs@bx.psu.edu_ Jen Galaxy team On 10/22/13 5:42 AM, Elwood Linney wrote:
After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy.
I had this problem with histories developed before the move and histories developed after the move.
I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC.
I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories.
Is anyone else having this problem? And found a solution?
Elwood Linney
___________________________________________________________ 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:
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-- Jennifer Hillman-Jackson http://galaxyproject.org
Hi Elwood, Jeremy and I took at a look at this. The failures in your history with this message: Error: number of labels must match number of conditions ...are due to a regression in the cuffdiff tool which Jeremy has just fixed. Some characters such as spaces in the condition name were valid prior to the move, but after the move they became invalid. They should now be valid once again. You've got one tophat job running and a cuffdiff job queued, and the rest of your grey datasets are waiting for those two jobs to be finished before they'll be queued (we'll be working on creating a visual distinction for this). I fixed the queued cuffdiff job, which I believe should allow it to run without error (or at least, not the same error). --nate On Oct 22, 2013, at 9:56 AM, Jennifer Jackson wrote:
Elwood,
Would you please share:
1. an original history that worked (if possible) 2. the workflow you are using and let me know how you generated (did you extract it recently (last week or so)? 3. problem history
There are a few known issues in here, some mitigated, one that has to do with extracted workflows from existing older histories that is Cuffdiff specific (actually, a few problems, found another last night). I want to rule those out or at least try to provide feedback.
I am at a conference over next several days, so let's use galaxy-bugs as a cc whenever we communicate so nothing is left lingering, plus I know Nate was looking into some of your data. Jeremy may jump also in at any time and help - he is the author of the wrapper.
So, in your reply, remove galaxy-user@bx.psu.edu and add galaxy-bugs@bx.psu.edu
Jen Galaxy team
On 10/22/13 5:42 AM, Elwood Linney wrote:
After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy.
I had this problem with histories developed before the move and histories developed after the move.
I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC.
I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories.
Is anyone else having this problem? And found a solution?
Elwood Linney
___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson
http://galaxyproject.org ___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
thank you all, its clearly working now and that is coming just in time, the results of two of these datasets will help us plan our next experiments for capping up a manuscript or two el linney On Tue, Oct 22, 2013 at 12:03 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Elwood,
Jeremy and I took at a look at this. The failures in your history with this message:
Error: number of labels must match number of conditions
...are due to a regression in the cuffdiff tool which Jeremy has just fixed. Some characters such as spaces in the condition name were valid prior to the move, but after the move they became invalid. They should now be valid once again.
You've got one tophat job running and a cuffdiff job queued, and the rest of your grey datasets are waiting for those two jobs to be finished before they'll be queued (we'll be working on creating a visual distinction for this). I fixed the queued cuffdiff job, which I believe should allow it to run without error (or at least, not the same error).
--nate
On Oct 22, 2013, at 9:56 AM, Jennifer Jackson wrote:
Elwood,
Would you please share:
1. an original history that worked (if possible) 2. the workflow you are using and let me know how you generated (did you extract it recently (last week or so)? 3. problem history
There are a few known issues in here, some mitigated, one that has to do with extracted workflows from existing older histories that is Cuffdiff specific (actually, a few problems, found another last night). I want to rule those out or at least try to provide feedback.
I am at a conference over next several days, so let's use galaxy-bugs as a cc whenever we communicate so nothing is left lingering, plus I know Nate was looking into some of your data. Jeremy may jump also in at any time and help - he is the author of the wrapper.
So, in your reply, remove galaxy-user@bx.psu.edu and add galaxy-bugs@bx.psu.edu
Jen Galaxy team
On 10/22/13 5:42 AM, Elwood Linney wrote:
After successfully using RNAseq software in Galaxy online for about 10
different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy.
I had this problem with histories developed before the move and
histories developed after the move.
I have had this problem using an order cuffmerge gtf file that worked
in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC.
I don't know if this is just some interface problem with a different
version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories.
Is anyone else having this problem? And found a solution?
Elwood Linney
___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson
http://galaxyproject.org ___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
This is great news, thanks for letting us know. --nate On Oct 22, 2013, at 2:34 PM, Elwood Linney wrote:
thank you all, its clearly working now and that is coming just in time, the results of two of these datasets will help us plan our next experiments for capping up a manuscript or two
el linney
On Tue, Oct 22, 2013 at 12:03 PM, Nate Coraor <nate@bx.psu.edu> wrote: Hi Elwood,
Jeremy and I took at a look at this. The failures in your history with this message:
Error: number of labels must match number of conditions
...are due to a regression in the cuffdiff tool which Jeremy has just fixed. Some characters such as spaces in the condition name were valid prior to the move, but after the move they became invalid. They should now be valid once again.
You've got one tophat job running and a cuffdiff job queued, and the rest of your grey datasets are waiting for those two jobs to be finished before they'll be queued (we'll be working on creating a visual distinction for this). I fixed the queued cuffdiff job, which I believe should allow it to run without error (or at least, not the same error).
--nate
On Oct 22, 2013, at 9:56 AM, Jennifer Jackson wrote:
Elwood,
Would you please share:
1. an original history that worked (if possible) 2. the workflow you are using and let me know how you generated (did you extract it recently (last week or so)? 3. problem history
There are a few known issues in here, some mitigated, one that has to do with extracted workflows from existing older histories that is Cuffdiff specific (actually, a few problems, found another last night). I want to rule those out or at least try to provide feedback.
I am at a conference over next several days, so let's use galaxy-bugs as a cc whenever we communicate so nothing is left lingering, plus I know Nate was looking into some of your data. Jeremy may jump also in at any time and help - he is the author of the wrapper.
So, in your reply, remove galaxy-user@bx.psu.edu and add galaxy-bugs@bx.psu.edu
Jen Galaxy team
On 10/22/13 5:42 AM, Elwood Linney wrote:
After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy.
I had this problem with histories developed before the move and histories developed after the move.
I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC.
I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories.
Is anyone else having this problem? And found a solution?
Elwood Linney
___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson
http://galaxyproject.org ___________________________________________________________ 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:
To search Galaxy mailing lists use the unified search at:
participants (4)
-
Elwood Linney -
Jennifer Jackson -
Jeremy Goecks -
Nate Coraor