Dear Galaxy, I know this issue has been discussed multiple times but I think what I'm trying to do is a little bit different and I wanted to see if it is viable.
Some time ago, I used bowtie and the included index for Mus musculus to do an alignment. Now I'm looking to use Cufflinks/compare/diff for expression. I annotated my alignments(SAM files) with the gff's found here:
ftp://biomirror.aarnet.edu.au/biomirror/ncbigenomes/M_musculus/special_requests/gff3/
I've tried running Cufflinks but have gotten 0 FPKM for all genes when using a reference like Ensembl, UCSC, etc. If I were to upload the gff's I posted here, concatenate them, and then try and use that as the reference, would it work? I'm going to try but just thought I'd throw it out there first. The main issue is that in my SAM/BAM files the annotations are GenBank Id's, gi|#|, and all other references I tried were with chr1 and the such. Now that I think about it, I might try just downloading the NCBI gtf from iGenomes. Regardless, let me know what you think! Thanks!