Converting Pileup Files To Wig/Bigwig

Question: Converting Pileup Files To Wig/Bigwig

7.9 years ago by

Hi, I was wondering if you have a tool that converts pileup files to variable step wigs so I can view coverage on UCSC. At present I have a rnaseq data mapped using bowtie. I've converted them to bam and generated pileups. thanks -- Swathi A. Kumar Interdepartmental Program in Genetics Center for Comparative Genomics Huck Institute of Life Science email : sak980@psu.edu tel : +1 814 441 8120

alignment bowtie • 2.7k views

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modified 7.9 years ago • written 7.9 years ago by Swathi Ashok Kumar • 20

7.9 years ago by

Loraine, Ann • 150

United States

Loraine, Ann • 150 wrote:

Hi, If you are mainly interested in viewing coverage, the pileup format may be overkill, since it captures base frequencies per position. The BowTie/TopHat source code distribution includes a program called łwiggles˛ that accepts a łSAM˛ format file and converts it to a łwig˛ file. Išve mainly looked at wiggles-generated files in Integrated Genome Browser bioviz.org/igb) but Išm sure they can work fine in the UCSC browser, as well. A student who works with me made a small change to łwiggles˛ that lets you run it like so: samtools view accepted_hits.bam | wiggles > coverage.wig If you would like him to send it to you, let me know! Best, Ann Loraine -- 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

ADD COMMENT • link written 7.9 years ago by Loraine, Ann • 150

Please note the graphing formats you can use at UCSC: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_f ormat bigWig format is most efficient. --Hiram

ADD REPLY • link written 7.9 years ago by Hiram Clawson • 260

7.9 years ago by

Swathi Ashok Kumar • 20

Swathi Ashok Kumar • 20 wrote:

Can it be integrated into galaxy ? I found another tool that does this at http://galaxy.fml.mpg.de/Under their SAM tools they have a pileup to wiggle conversion tool I can't find any mention of a program called 'wiggles' in the source

ADD COMMENT • link written 7.9 years ago by Swathi Ashok Kumar • 20

There are no plans to integrate this tool into Galaxy's main server. However, should someone outside of the Galaxy team write a patch to integrate this tool into Galaxy, they could share it via or community site ( http://community.g2.bx.psu.edu/ ) and we would consider adding it to our public server. I'd recommend copying your dataset to the *.de server, performing the conversion, and then copying the converted dataset back to the main server. (Using the 'paste URL' and/or FTP upload option, you should be able to copy datasets between Galaxy instances. To copy a dataset between Galaxy servers, copy the URL for a dataset from the 'source' server into the upload form in the 'destination' server and click 'upload') Thanks, J.

ADD REPLY • link written 7.9 years ago by Jeremy Goecks • 2.2k

7.9 years ago by

Nick Schurch • 50

Nick Schurch • 50 wrote:

HI, I can't find any mention of a program called 'wiggles' in the source code distribution of bowtie 0.12.7, or out install of 0.12.3. Could someone point me to the location of the program in the bowtie file structure, or failing that a website for it? -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893

ADD COMMENT • link written 7.9 years ago by Nick Schurch • 50

wiggles is in the Tophat distribution, not the Bowtie distribution. Thanks, J.

ADD REPLY • link written 7.9 years ago by Jeremy Goecks • 2.2k

My apologies. I mis-spoke. (Mis-typed?) The wiggles program is in the TopHat distribution: $ ls AUTHORS fix_map_ordering sam_juncs COPYING gtf_juncs segment_juncs README juncs_db sra_to_solid bed_to_juncs library_stats tophat closure_juncs long_spanning_reads tophat_reports contig_to_chr_coords mask_sam wiggles extract_reads prep_reads Very sorry for the mixup. I am cc-ing Adam Baxter, who modified wiggles to run like so: samtools view accepted_hits.bam | wiggles > coverage.wig If you would like a copy of his modified version, feel free to contact him directly. -Ann

ADD REPLY • link written 7.9 years ago by Loraine, Ann • 150

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