HI, The option you need in IGV tools is "count". You set a window size and this gives you a tdf file from your sorted bam (or sam) file which is nice and quick to view on IGV.
Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 22 Feb 2011, at 15:52, Ying Zhang wrote: > Dear David: > > thank you very much for helping me! > > I have download the IGV and I do find the IGVtools, however, I am not sure > which > tool I should use for generate a tdf file, the tile function will generate a > tdf > file, but the input file format does not include bam or sam file, instead it > need wig file. But I have no wig file to put in. So I am wondering whether you > need to use other tool first. I really appreciate your help! Thank you very > much! > > Best > > Ying > > Quoting David Matthews <d.a.matth...@bristol.ac.uk>: > >> 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/ >> >> >> _______________________________________________ >> 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/
