Re: [galaxy-user] get wig file after tophat
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-datase... 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.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 Galaxy lists, please use the interface at:
-- 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:
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
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-datase...
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.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 Galaxy lists, please use the interface at:
-- 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:
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:
participants (2)
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Brad Chapman -
Jeremy Goecks