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!

-- 
Richard Linchangco
PSM in Bioinformatics
College of Computing and Informatics
University of North Carolina at Charlotte
Tel: (630)440-7010
rlinc...@uncc.edu, rlin...@gmail.com
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