Hi, Galaxy user.
I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to
check differential expressed genes in my samples.
I have 3 normals and 6 cancers samples, I did the following:
- After tophat for each samples, run cufflink with refseq annotation which
has 25266 genes and 43091 transcripts
- cuffmerge all cufflink outputs contains 58112 lines
- run cuffdiff with 3 normals as triplicate and compare to each cancer
Suprisingly, I fould out that the tanscripts tracking file, gene tracking,
CDS tracking only has 2000 genes and 4000 transcripts. So the cufflink only
compare 2000 genes and 4000 transcripts between samples.
The question I want to ask here is that *why are the rest of the genes and
transcripts not being tested and included in the tracking files?* Do you
know what cause this kind of problem?
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: