I'm a fan of viewing "coverage.wig" files - they give a nice summary of read
distribution over a chromosome.

What I like about the "coverage.wig" file is that it captures the full read
depth at every base. TDF does something different - it summarizes over
(relatively) large regions. (But this can be useful, too!)

If you use Integrated Genome Browser (bioviz.org/igb) you can open the
"coverage.wig" file and view it directly.

I'm a bit biased of course -- my lab contributes to IGB -- but I think you
would like how it handles "wig" and short read alignment "bam" files.

I wrote some documentation about "wig" files on the IGB Users Guide Web
site. If you have any questions, let us know - we are happy to help:

Opening "wig" files in IGB
https://wiki.transvar.org/confluence/x/w4BJAQ

Galaxy is a such an accessible resource -- we are trying hard to make IGB
(and all the tools we develop!) as easy to use and intuitive as Galaxy.

Very best wishes,

Ann




On 2/21/11 5:35 PM, "David Matthews" <d.a.matth...@bristol.ac.uk> wrote:

> 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/
> 

-- 
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/

Reply via email to