Hello,
The transcript name when using RefSeq as a reference annotation is the "NM_" type of identifier.
If you want to include a gene symbol, then the reference annotation should include the attribute "gene_name". The iGenomes GTF files are an example of datasets that include this attribute.
http://wiki.galaxyproject.org/Support#Interpreting_scientific_results See: /Example/?/*RNA-seq analysis*/*tools* http://cufflinks.cbcb.umd.edu/faq.html#gtfs http://cufflinks.cbcb.umd.edu/igenomes.html http://cufflinks.cbcb.umd.edu/manual.html (search on page for "gene_name" to see where can be used/output)
Best,
Jen Galaxy team
On 11/12/13 10:40 AM, Irene Bassano wrote:
Dear Jennifer, I am about to start a new analysis and learning from my old mistakes would like to ask just one question: I would like my Cufflinks and Cuffdiff results to give me the actual gene name or transcript name rather than "NM_......" like I had last time i run the job.
At which stage and which option do I have ti use to get the proper names?
Thanks a lot!
Irene
Hello,
Could you please advise me on this probably naive question. When I compare sample A and sample B by Ciffdiff and then separately compare Sample A to Sample C by Cuffdiff too, should the FMPK value be the same for A in both tests? At the moment mine does not seem to be!
Best wishes
Clare
Hi Noa,
Yes I did use Cufflinks so this sounds just like my problem. So how have you dealt with the problem?
Best wishes,
Clare
On 14 Nov 2013, at 18:17, Noa Sher wrote:
Hi Clare We just ran into a similar issue about a week ago and were debugging with the authors of cuffdiff Apparently there are issues with the -b parameter - were you using this in cufflinks? If yes - this may be the cause - we switched the order of the replicates and the values changed; as did PCA's of the samples, etc They are working on this issue for an upcoming version of cufflinks. I am interested in knowing whether this was indeed your problem or were you using a pipeline that does not include cufflinks? Good luck, Noa
On 14/11/2013 13:13, clare Hardman wrote:
Hello,
Could you please advise me on this probably naive question. When I compare sample A and sample B by Ciffdiff and then separately compare Sample A to Sample C by Cuffdiff too, should the FMPK value be the same for A in both tests? At the moment mine does not seem to be!
Best wishes
Clare
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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Dont use the - b parameter
Sent from my iPhone; please excuse any brevity or typos!
On Nov 15, 2013, at 2:51 PM, clare Hardman chardman@mrc-lmb.cam.ac.uk wrote:
Hi Noa,
Yes I did use Cufflinks so this sounds just like my problem. So how have you dealt with the problem?
Best wishes,
Clare
On 14 Nov 2013, at 18:17, Noa Sher wrote:
Hi Clare We just ran into a similar issue about a week ago and were debugging with the authors of cuffdiff Apparently there are issues with the -b parameter - were you using this in cufflinks? If yes - this may be the cause - we switched the order of the replicates and the values changed; as did PCA's of the samples, etc They are working on this issue for an upcoming version of cufflinks. I am interested in knowing whether this was indeed your problem or were you using a pipeline that does not include cufflinks? Good luck, Noa
On 14/11/2013 13:13, clare Hardman wrote:
Hello,
Could you please advise me on this probably naive question. When I compare sample A and sample B by Ciffdiff and then separately compare Sample A to Sample C by Cuffdiff too, should the FMPK value be the same for A in both tests? At the moment mine does not seem to be!
Best wishes
Clare
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:
galaxy-user@lists.galaxyproject.org
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