I can answer IGV questions, sadly I'm still coming up to speed on Galaxy. I've lost track of the original question, but IGV computes a coverage histogram on the fly, a bit like the Galaxy Track Browser, but you have to be zoomed in. However, you can also precompute a coverage histogram for the whole genome with "igvtools", a command line package. Its in a binary format (tdf) that can support viewing at any resolution in IGV. Finally, you can use igvtools to compute this as a standard "wig" file, just supply ".wig" as the extension instead of ".tdf". This is not as efficient as TDF but you can use it in other browsers, such as Galaxy and IGB. Best, Jim
Hi Ying,
You're in luck because I've been working with genome browsers lately, so I think I can help you address your problem. What you're looking for is a visualization of a coverage histogram for the BAM reads produced by Tophat, yes?
It turns out that some genome browsers provide this automatically as part of their solution for visualizing BAM files b/c BAM files tend to be very large and hence visualizing aggregated data is often the best solution. Both IGV and the Galaxy Trackster Browser support this functionality. I think you'll have to do some simple file conversions to get the display you want in IGV; you can check out the IGV documentation or perhaps Jim can help. I'm not sure if IGB supports this visualization mode for BAM; Ann can chime in with additional information.
The Galaxy Track Browser supports coverage histograms when viewing large regions. When zoomed in, the reads are typically displayed individually, although there is a (very beta) option to create a histogram for the visible set of reads; this option may not work well (yet!) as Tophat reads often have large gaps.
The top track in this visualization shows a coverage histogram for a set of Tophat reads:
http://test.g2.bx.psu.edu/u/jeremy.goecks/v/assembly-of-h1-hesc-rna-seq-data
Please see my previous email to Vasu for details about setting up a visualization in the Galaxy Track Browser.
Best, J.
On 4/20/11 5:16 PM, "Ying Zhang" <ying.zhang.yz323@yale.edu> wrote:
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:
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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:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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
-- 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. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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