Hi,

You can get an equivalent visualisation from the IGV viewer by the Broad 
Institute - its under IGV tools and generates a tdf file from bam or sam files. 
This also gives a quick and easy way of looking at depth at any particular site 
and is very accessible.

Cheers
David


On 21 Feb 2011, at 21:44, Jeremy Goecks wrote:

> Hi all,
> 
> Ann is correct - Tophat does not produce .wig files when run anymore. 
> However, it's fairly easy to use Galaxy to make a wiggle-like coverage file 
> from a BAM file:
> 
> (a) run the pileup tool on your BAM to create a pileup file;
> (b) cut columns 1 and 4 to get your coverage file.
> 
> A final note: it's often difficult to visualize coverage files because 
> they're so large. You might be better off visualizing the BAM file and using 
> the coverage file for statistics.
> 
> Best,
> J.
> 
>> Hello,
>> 
>> 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,
>> 
>> Ann Loraine
>> 
>> 
>> On 2/21/11 3:39 PM, "Ying Zhang" <ying.zhang.yz...@yale.edu> wrote:
>> 
>>> Hi:
>>> 
>>> 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!
>>> 
>>> Best
>>> 
>>> 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:
>>> 
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>> 
>>> To manage your subscriptions to this and other
>>> Galaxy lists, please use the interface at:
>>> 
>>> http://lists.bx.psu.edu/
>> 
>> -- 
>> Ann Loraine
>> Associate Professor
>> Dept. of Bioinformatics and Genomics, UNCC
>> North Carolina Research Campus
>> 600 Laureate Way
>> Kannapolis, NC 28081
>> 704-250-5750
>> www.transvar.org
>> 
>> 
>> _______________________________________________
>> 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:
>> 
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other
>> Galaxy lists, please use the interface at:
>> 
>> http://lists.bx.psu.edu/
> 
> 
> _______________________________________________
> 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:
> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/


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