Hello Lizex,
The primary reason why runs fail is the input data format. A double
check that the reference genome identifiers are the same between the BAM
files and any reference GTF files would be recommended. This and other
common issues are covered in our FAQ here:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
If you think that the Tophat run was a problem, then contacting the tool
authors at tophat.cuffli...@gmail.com is the best way to get help with a
Tophat issue, especially if run line-command outside of Galaxy.
http://tophat.cbcb.umd.edu/
http://cufflinks.cbcb.umd.edu/
If you are still stuck, please send a bug report using the green bug
icon for the error dataset and we can take a look. Please put in a note
if the email address for your Galaxy account is different than this one.
Thanks!
Jen
Galaxy team
On 11/7/11 11:33 PM, Lizex Husselmann wrote:
Hi
I've started an alignment using the command line (Tophat v1.3.3). I've
uploaded the files (accepted.bam) onto Galaxy and upon doing the
Cufflinks analysis on the Galaxy interface, it shows an error. I had to
look at the options. I've change the options to default and run it again
but still the same error. Is the accepted.bam file not compatible with
the Galaxy Cufflinks? Is there something I not doing?
Kind regards
Lizex
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