Re: [galaxy-user] Converting pileup files to wig/bigwig
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
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?
wiggles is in the Tophat distribution, not the Bowtie distribution. Thanks, J.
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 On Wed, Jan 12, 2011 11:01 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
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?
wiggles is in the Tophat distribution, not the Bowtie distribution.
Thanks, J. _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Can it be integrated into galaxy ?
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 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'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.
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 On 1/12/11 10:50 AM, "Nick Schurch" <N.Schurch@dundee.ac.uk> 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?
participants (4)
-
Ann Loraine -
Jeremy Goecks -
Nick Schurch -
Swathi Ashok Kumar