I was wondering how to get gene "name" annotated to the cuffdiff. I used mm10 as the template, and used "UCSC Main on Mouse: ensGene (genome)" as the GTF files when I am doing cuffmerge. However, the document for cuffdiff is still not annotated with gene names. I know people have asked similar question, but I still can't really get the gene name annotated with the answers. i was wondering if someone could help me with it
The reference annotation source must include the gene_name attribute for this information to be incorporated. iGenomes has a GTF for mm10 with this attribute. Download the tar file, uncompress it, then load just the genes.gtf file up to Galaxy and use that instead of the annotation from UCSC.
iGenomes source data: https://support.illumina.com/sequencing/sequencing_software/igenome.html
Thanks! Jen, Galaxy team