Ying and all;
Nice discussion and lots of great ideas. One other approach is to generate
bigWig files. You can serve these directly from Galaxy and they have
the same advantages as BAM files; they are compressed and individual
regions that be fetched on demand by UCSC.

This tool in the community tool shed creates bigWig coverage files 
directly from BAM alignments:

http://bit.ly/fxnUJ3

Brad

> Ying,
> 
> You can create a coverage file from a BAM file using this workflow:
> 
> http://main.g2.bx.psu.edu/u/jeremy/w/create-coverage-dataset-from-bam-dataset
> 
> While this doesn't generate a proper wiggle file, it can be a useful file for 
> statistical analysis.
> 
> I and others have suggested ways to visualize a BAM file with coverage data 
> in mind: Trackster, IGV, and IGB.
> 
> Thanks,
> J.
> 
> On Feb 22, 2011, at 11:04 AM, Ying Zhang wrote:
> 
> > Dear Jeremy:
> > 
> > Thank you so much for helping me!
> > 
> > Followed your instructions, I do get the pileup file, however, I am a 
> > little bit
> > confused about how you generate the wig file. So you mean to cut out the 
> > column
> > 1 and 4, and use the rest of them to generate the wig file or cut the 
> > columns 1
> > and 4 and past it to another file to generate the wig file? The reason I am
> > asking is that it looks like column 1 is the information of chromosome, I am
> > not sure whether I should cut it out. Also I found out that the pileup file 
> > is
> > kind of big, so how you can cut the column 1 and 4? do you need to run a
> > command? I am basically not an expert in computer, do you know whether 
> > there is
> > an easy way to do this task in windows? THank u so much!
> > 
> > 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
> 
> 
> _______________________________________________
> 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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