[BioC] DiffBind for Galaxy

[Dan Tenenbaum]

----- Original Message -----
> From: "Rory Stark" <Rory.Stark at cruk.cam.ac.uk>
> To: "Christoph Grunau" <christoph.grunau at univ-perp.fr>
> Cc: bioconductor at r-project.org
> Sent: Tuesday, September 17, 2013 9:17:48 AM
> Subject: Re: [BioC] DiffBind for Galaxy
> 
> Hi Christoph-
> 
> Are the aligned read files you are using actually in BED format (chr,
> start, end, name, score, strand)?
> 
> I'll look into adding an option to allow a .dat extension as an
> alternative to .bed; if it is easy (and Gord has time) I'll try to
> have it
> in the 2.13 release.
> 
> Cheers-
> Rory
> 
> 
> On 17/09/2013 16:23, "Christoph Grunau"
> <christoph.grunau at univ-perp.fr>
> wrote:
> 
> >Dear Rory,
> >
> >thank you very much for your DiffBind software. It s actually the
> >only
> >software that allows us to identify differentially modified regions
> >in
> >ChIPseq against histone isoforms. I use it a lot and I would like to
> >share it with my colleagues via our local Galaxy instance.
> >Unfortunately,
> >there is one mayor obstacle. As you will know, galaxy files have the
> >uniform .dat suffixe. 

I dont' believe this is the case; I think you can specify any suffix in the $GALAXY_HOME/datatypes_conf.xml file,
which already seems to be aware of .bed and .bam extensions.

Dan


>  However for DiffBind bamReads and bamControl
> >file
> >format is detected via suffixes that must be bed, bam or bed.gz
> >
> >dba.count
> >
> >Count reads in binding site intervals
> >
> >Description
> >Counts reads in binding site intervals. Files must be one of bam,
> >bed and
> >gzip-compressed bed. File
> >suffixes must be ".bam", ".bed", or ".bed.gz" respectively.
> >
> >I solved this issue by creating a copy of the .dat file with suffix
> >.bed.
> >However, this slows down the analysis and generates redundancy for
> >files
> >that are relatively large. Would it be possible to modify your code
> >so
> >that the file format of bamReads and bamControl can be transmitted
> >as
> >parameter similar to what is used for loading the peakset?
> >I know I ask a lot but this modification would be tremendously
> >helpful.
> >
> >Many thanks and very best regards
> >
> >Christoph Grunau
> >
> >
> >--
> >Christoph Grunau
> >Prof. des Universités/Professor (HDR)
> >Université de Perpignan Via Domitia
> >UMR 5244 CNRS Ecologie et Evolution des Interactions (2EI)
> >52, avenue Paul Alduy
> >66860 PERPIGNAN Cedex
> >France
> >Tel 33 (0)4.68.66.21.80
> >Fax 33 (0)4.68.66.22.81
> >http://2ei.univ-perp.fr/
> >http://methdb.univ-perp.fr/epievo/
> >
> >
> >
> 
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