Dear Ann and Jeremy:

We have this discussion long time ago, and I am sorry that I brought it
up here
again. I am just thinking that as Ann said, can we add this tool which convert
bam into wig file into galaxy? Or make a workflow to generate a wig
file from a
bam file generate by tophat? In this way we can just easily get a wig
file from
galaxy and will be able to see it in IGB. I know this may seems
unnecessary for
the purpose of statistical analysis, but if we can see the coverage with IGB,
sometimes it is helpful to pick up interesting points quickly for specific
genes. This may seems a old fashion way but my boss is a big fan of using IGB
to see expression file(wig or sgr file) and do some analysis. THanks a lot!

BEst

Ying

Quoting Jeremy Goecks <jeremy.goecks@emory.edu>:

> 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.yz323@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
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>>
>> --
>> 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/
>

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
___________________________________________________________
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