Hello Richard,
The best way is evaluate the file is to compare them with the
specifications in the Cufflinks documentation
(http://cufflinks.cbcb.umd.edu/gff.html) and then to run them through
the tool. However, I can let you know that from a quick look, many of
the key attributes are not in these files (transcript start site, gene
name).
This is one of the areas that can be the trickiest to get working.
Identifiers (specifically chromosome identifiers) much be exact, file
formats must be in spec, and their are certain attributes in the GTF/GFF
files that Cufflinks will take advantage of if present (and ignore if not).
The issues with the UCSC and Ensembl GTF files and Cufflinks was also
likely with missing attributes in the ninth field. iGenomes does have
datasets that were specifically annotated to have a full compliment of
these attributes. You can use either UCSC's data for mm9 or mm10 at
Galaxy (mm10 is new in Galaxy - today! - so you would need to run TopHat
again).
http://cufflinks.cbcb.umd.edu/igenomes.html
Best,
Jen
Galaxy team
On 6/6/12 12:32 PM, Richard Linchangco wrote:
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!
--
Jennifer Jackson
http://galaxyproject.org
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