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.yz...@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.goe...@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.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/ >>> >> >> >> >> 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: 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/
