From tbooth at ceh.ac.uk  Wed Dec  7 11:42:08 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 07 Dec 2011 16:42:08 +0000
Subject: [Bio-Linux] New and updated packages in Bio-Linux: Catchall + Mira
 + Mothur + Artemis/ACT
Message-ID: <1323276128.24068.4698.camel@barsukas.nwl.ac.uk>

Dear Bio-Linux Users,

This is just to draw your attention to some of the packages in Bio-Linux
have been added or updated recently.  As ever, to ensure you have the
package installed:

        sudo apt-get update
        sudo apt-get-install bio-linux-packagename
        (replacing packagename with the app you want - all lowercase)

* catchall - This is a new program for analyzing data derived from
experiments or observations of species abundances or multiple recapture
counts.  See: http://www.northeastern.edu/catchall

        NB: If you install this package, to run the program you simply
        need to type "catchall <args ...>", not "mono CatchAllcmdL.exe
        <args ...>" as stated in the official manual.
        
* mothur has now been updated to v1.22.2.  If the new bio-linux-catchall
package is installed, the catchall() feature in Mothur should work as
advertised.

* mira is now updated to 3.4.0 with support for assembly of Ion Torrent
reads.

* artemis has been updated to the latest release 13.2.0.  This update
also includes the latest ACT

Any bug reports to the helpdesk address please: helpdesk at nebc.nerc.ac.uk

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

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From sgrannem at staffmail.ed.ac.uk  Wed Dec 14 07:52:39 2011
From: sgrannem at staffmail.ed.ac.uk (Sander Granneman)
Date: Wed, 14 Dec 2011 12:52:39 +0000
Subject: [Bio-Linux] beta testers for pyCRAC,
	a set of user-friendly python tools for CLIP/CRAC data analyses
Message-ID: <11A786DD-C9EF-4B38-8FD7-520A64C816B8@staffmail.ed.ac.uk>

Hi All,

The CLIP and related CRAC techniques allow researchers to identify direct protein-RNA interactions in vivo and can be used in combination with high-throughput sequencing to get a comprehensive map of protein-RNA interactions transcriptome-wide. CLIP/CRAC data differ in many respects from data generated by transcriptome analysis or genome resequencing. These data analyses involved development of many new algorithms to extract all the relevant information and generation of new data processing pipelines. Many laboratories have expressed an interest in using the technique but were deterred by their lack of experience in tackling the CLIP/CRAC high-throughput datasets.

I am in the process of developing a python framework tailored to tackle CLIP/CRAC datasets and other directional RNAseq data. Using this foundation I have written a number of user-friendly (and hopefully intuitive) tools for the analysis of CRAC/CLIP datasets, including tools for motif searches on clusters, filtering reads based on the presence of mutations, generating pileups and multiple sequence alignments, tools for making genome browser compatible files, etc etc. The package also contains several modules (GTF2 parser, SAM/Novoalign single and paired-end parsers) which could be used for the rapid development of new scripts.

All the tools have detailed help menus and I have written an draft manual. 

I am looking for people who would be interested in testing these tools and I'm keen for some feedback. 

If you are interested in testing the package, please drop me an e-mail!

Sander

------------------------------------------------------------------
Sander Granneman, PhD
Wellcome Trust RCD Fellow
Institute for Structural and Molecular Biology
Centre for Systems Biology at Edinburgh (CSBE)
Room 3.06, CH Waddington Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JD

Phone:
office: +44 (0) 131 651 9082
lab:	+44 (0) 131 651 9055

sgrannem at staffmail.ed.ac.uk

http://sandergranneman.bio.ed.ac.uk
http://www.csbe.ed.ac.uk/
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