Question: Cufflinks Display In Ucsc
0
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Rich,
Without seeing your data, it sounds as if the formatting of the file
is
corrupted. You may try using one of Galaxy's data transformation tools
(GFF-to-BED) to see if that offers any clues, or a GFF or GTF file
format validator (there are several offered online, I believe that
UCSC
also has one in their tool kit).
If this is direct output from Cufflinks, contacting the tool authors
to
ask if this is expected output is another good place to check. Contact
information is in this section of our support wiki:
http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result
If all of this checks out, you may also want to contact UCSC to ask if
there are any known limitations with display of RNA-seq data. As an
alternative, the Trackster visualization tool in Galaxy has become
quite
robust with several new features and may be what you are looking for.
It
has been tuned to work particularly well with RNA-seq data (with both
native and custom genomes). This would probably be my first choice as
a
test before going further. If Trackster produced an error with the
dataset, then there is definitely a problem with formatting. If
Trackster will display, then the problem may be with what UCSC is
expecting and what Cufflinks is producing or with some post-Cufflinks
processing.
Hopefully one of these will help discover the issue, but if you find
that you are still stuck after working through the problem, please
send
a shared history link to galaxy-bugs@bx.psu.edu and we can try to
provide feedback. Please include what you tested and the results so we
are in the same place and know what is working and what isn't.
Going forward, please try to send new questions as brand new threads
(not as replies to old threads with new subject lines) with the "to"
address directly to galaxy-user@bx.psu.edu (you do not need to include
me as a "to" or "cc"). This ensures that questions are not lost (as
this
one almost was) and that our entire team and community can contribute
to
and benefit from replies. I am sending this email now "to" galaxy-user
to start up a new thread and correct the tracking. Replies should now
be
sent to this message as "reply-all". Thanks for understanding! Makes
it
much easier for us and nothing (well, we try!) slips through.
Best,
Jen
Galaxy tem
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support