Get Gene Name From Cuffdiff'S Output?

Question: Get Gene Name From Cuffdiff'S Output?

5.5 years ago by

Hoang, Thanh • 200 wrote:

Hi guys, I am trying to examine gene differential expression in my mouse samples using : Cufflink >> Cuffmerge>>Cuffdiff The output from Cuffdiff shows only gene id, but not gene name: test_id gene_id genelocus sample_1 sample_2 XLOC_000001XLOC_000001- 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

rna-seq cuffmerge • 3.7k views

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modified 5.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.5 years ago by Hoang, Thanh • 200

5.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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.cufflinks@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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.5 years ago by Jennifer Hillman Jackson ♦ 25k

5.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, Yes, if not mapped against mm10, you will need to start from that step and work forward. 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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.5 years ago by Jennifer Hillman Jackson ♦ 25k

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