I think I know the answer (sort of) to this question.
This may be because newer versions of tophat stopped running the "wiggles"
program, which is still part of the tophat distribution and is the program
that makes the "coverage.wig" file.
A later version of tophat might bring this back, however - there's a note to
this effect in the tophat python code.
So if you can run wiggles, you can make the "coverage.wig" file on your own.
A student here at UNC Charlotte (Adam Baxter) made a few changes to the
"wiggles" source code that would allow you to use it with samtools to make a
"coverage.wig" file from the "accepted_hits.bam" file that TopHat creates.
If you (or anyone else) would like a copy, please email Adam, who is cc'ed
on this email.
We would be happy to help add it to Galaxy if this would be of interest to
you or other Galaxy users.
If there is any way we can be of assistance, please let us know!
Very best wishes,
On 2/21/11 3:39 PM, "Ying Zhang" <ying.zhang.yz...@yale.edu> wrote:
> I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out
> that after the tophat analysis, we can not get the wig file from it anymore
> which is used to be able to. Do you have any idea of how to still be able to
> get the wig file after tophat analysis? Thanks a lot!
> Ying Zhang, M.D., Ph.D.
> Postdoctoral Associate
> Department of Genetics,
> Yale University School of Medicine
> 300 Cedar Street,S320
> New Haven, CT 06519
> Tel: (203)737-2616
> Fax: (203)737-2286
> The Galaxy User list should be used for the discussion
> of Galaxy analysis and other features on the public
> server at usegalaxy.org. 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:
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. 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: