Hi Galaxy Support,
I want to use cufflinks to quantify my own bam file, which is not from galaxy tophat. I tried several times but failed to get id. I can get fpkm. I import hg19 gtf file from ucsc. This time I got gene-id but all fpkm is 0. I am really frustrated with this. Please give me some instruction about setting parameters.
This is the latest setting. I still got CUFF.id instead of refseq id or gene id. Anyone can help me?
The reference GTF was from UCSC? Then it does not contain the attributes that Cuffdiff requires for certain key functions.
The most direct way to obtain a GTF reference annotation file that contains the key attributes is to use the version from iGenomes. Download the tar file locally, unpack it, and then upload the genes.gtf dataset to Galaxy for use with these tools.
A description of these attributes and how they are used by Cuffdiff is in the manual here: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#cuffdiff-input-files