[galaxy-user] Get Gene name from Cuffdiff's output?
Hi guys, I am trying to examine gene differential expression in my mouse samples using : Cufflink CuffmergeCuffdiff The output from Cuffdiff shows only gene id, but not gene name: test_id gene_idgenelocussample_1 sample_2 XLOC_01XLOC_01- 1:3200263-3200566EpitheliumFiber Could anyone tell me how to make the gene name show up? I used Mus_musculus.GRCm38.71.dna.toplevel.fa as the reference sequence (not GRCm38/mm10 from UCSC table broswer because i think this may be old version). I have been trying to find a solution online but still very confused Thanks so much Thanh ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Get Gene name from Cuffdiff's output?
Hello Thanh, These attributes would come from the reference GTF or GFF3 file that you are using (not the reference genome). It looks like you are not using one, or that it did not cover this particular gene bound. The iGenomes GTF files are preferred as they contains all of the attributes that will both populate these sorts of values, but also allow the full compliment of statistics to be generated by the tool package. This is explained in the tool's manual: http://cufflinks.cbcb.umd.edu http://cufflinks.cbcb.umd.edu/ http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server That said, I don't think there is an iGenomes GTF for the reference genome you have selected. I am not aware of a liftOver file either (but I could be wrong, you can ask UCSC). You also could try posting a question to the tophat.cuffli...@gmail.com google group to see what others are using/what is available right now. It may come down to choosing which is more important for your project - the most current genome or better annotation. Good luck! Jen Galaxy team On 6/17/13 11:13 AM, Hoang, Thanh wrote: Hi guys, I am trying to examine gene differential expression in my mouse samples using : Cufflink CuffmergeCuffdiff The output from Cuffdiff shows only gene id, but not gene name: test_id gene_id gene locus sample_1 sample_2 XLOC_01 XLOC_01 - 1:3200263-3200566 Epithelium Fiber Could anyone tell me how to make the gene name show up? I used Mus_musculus.GRCm38.71.dna.toplevel.fa as the reference sequence (not GRCm38/mm10 from UCSC table broswer because i think this may be old version). I have been trying to find a solution online but still very confused Thanks so much Thanh ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Get Gene name from Cuffdiff's output?
Hello, On 6/17/13 12:24 PM, Hoang, Thanh wrote: Hi Jen, Thank you very much for your quick response. I have just downloaded GTF file ( Mus musculus, UCSC, mm10) from iGenome. Correct me if I am wrong. I should start everything from the beginning again by uploading the GTF file to Galaxy via FTP uploading. Then, start mapping and assembly and analyzing the transcript using the GTF file this time : TopHat Cufflink Cuffmerge -Cuffdiff ??? Yes, if not mapped against mm10, you will need to start from that step and work forward. Also, do you know any good software to assign genes into functional groups ( Gene ontology) ? See the tool Phenotype Association - g:Profiler for one option. The UCSC Table browser may also offer GO annotation in a mm10 track that you can intersect or join your results to. Biomart's Unigene annotation is another great resource. Best, Jen Galaxy team Thank you so much for your help Thanh On Mon, Jun 17, 2013 at 2:30 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello Thanh, These attributes would come from the reference GTF or GFF3 file that you are using (not the reference genome). It looks like you are not using one, or that it did not cover this particular gene bound. The iGenomes GTF files are preferred as they contains all of the attributes that will both populate these sorts of values, but also allow the full compliment of statistics to be generated by the tool package. This is explained in the tool's manual: http://cufflinks.cbcb.umd.edu http://cufflinks.cbcb.umd.edu/ http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server That said, I don't think there is an iGenomes GTF for the reference genome you have selected. I am not aware of a liftOver file either (but I could be wrong, you can ask UCSC). You also could try posting a question to the tophat.cuffli...@gmail.com mailto:tophat.cuffli...@gmail.com google group to see what others are using/what is available right now. It may come down to choosing which is more important for your project - the most current genome or better annotation. Good luck! Jen Galaxy team On 6/17/13 11:13 AM, Hoang, Thanh wrote: Hi guys, I am trying to examine gene differential expression in my mouse samples using : Cufflink CuffmergeCuffdiff The output from Cuffdiff shows only gene id, but not gene name: test_id gene_id gene locus sample_1 sample_2 XLOC_01 XLOC_01 - 1:3200263-3200566 Epithelium Fiber Could anyone tell me how to make the gene name show up? I used Mus_musculus.GRCm38.71.dna.toplevel.fa as the reference sequence (not GRCm38/mm10 from UCSC table broswer because i think this may be old version). I have been trying to find a solution online but still very confused Thanks so much Thanh ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.org http://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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
