[Bio-linux-dev] tophat2

Tim Booth tbooth at ceh.ac.uk
Fri Dec 7 04:27:34 EST 2012


I hear you.  Am packaging bowtie2 as "bowtie2" and will let you know
when it's ready to install.

Cheers,

TIM

On Thu, 2012-12-06 at 22:23 +0000, Wagstaff, Simon wrote:
> Hi Tim, 
> I second Will's comments. Although there are improvements with speed
> and memory footprint of Bowtie2 over Bowtie, there are also important
> differences in the way Bowtie and Bowtie2 actually process the reads -
> see http://bowtie-bio.sourceforge.net/index.shtml. There are plenty of
> reasons why you might want to have both versions available for
> different analytical workflows. In essence they should be considered
> as different but related programs, rather than versions. Substituting
> Bowtie2 for Bowtie in established workflows may not necessarily give
> you what you expect.
> 
> 
> Am enjoying Biolinux 7 immensely.
> 
> 
> Cheers,
> 
> 
> Simon
> _________________________________
> 
> 
> Simon Wagstaff
> Tel: +44-(0)151-705-3164
> Fax: +44-(0)151-705-3371
> email: simonw at liv.ac.uk
> 
> 
> 
> 
> 
> On 6 Dec 2012, at 21:32, William Spooner wrote:
> 
> > Thanks Tim,
> > 
> > Actually, there is; bowtie2 is a big update and there are still
> > people who want to use the 'original' bowtie in established
> > workflows. I've found bowtie2 has a different memory profile which
> > can cause problems, but I expect it's worth it for the extra
> > sensitivity.
> > 
> > Will
> > 
> > On 6 Dec 2012, at 18:34, Tim Booth wrote:
> > 
> > > Hi Will,
> > > 
> > > Hmmm - they've renamed it from bowtie to bowtie2 so uscan didn't
> > > see
> > > that the new version was available.  I wonder if there's any
> > > reason you
> > > might want both at once?
> > > 
> > > I'll have a try rebuilding it now.
> > > 
> > > Cheers,
> > > 
> > > TIM
> > > 
> > > On Wed, 2012-12-05 at 22:56 +0000, William Spooner wrote:
> > > > Hi Tim,
> > > > 
> > > > Many thanks for taking care of this.
> > > > 
> > > > I've finally got around to trying it out. tophat seems to be the
> > > > at version 2 (as is cufflinks);
> > > > http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/
> > > > 
> > > > bowtie, however, is languishing on version 0;
> > > > http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/
> > > > 
> > > > Is this as expected?
> > > > 
> > > > Thanks,
> > > > 
> > > > Will
> > > > 
> > > > 
> > > > On 14 Nov 2012, at 14:48, Tim Booth wrote:
> > > > 
> > > > > Hi,
> > > > > 
> > > > > I've pushed the updates to all these and Velvet, so everything
> > > > > should be
> > > > > current now.
> > > > > 
> > > > > Cheers,
> > > > > 
> > > > > TIM
> > > > > 
> > > > > On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:
> > > > > > Many thanks Tim,
> > > > > > 
> > > > > > We'll test that tomorrow. I presume it's the complete
> > > > > > bowtie2/tophat2/cufflinks2 stack?
> > > > > > 
> > > > > > Will
> > > > > > 
> > > > > > On 13 Nov 2012, at 16:58, Tim Booth wrote:
> > > > > > 
> > > > > > > Hi Will,
> > > > > > > 
> > > > > > > The TopHat package maintained by Debian Med is up-to-date
> > > > > > > and seems to
> > > > > > > build fine on Ubuntu, so I've pushed a newer version to
> > > > > > > the Bio-Linux
> > > > > > > PPA.  Anyone who already upgraded to BL7 will get the
> > > > > > > update
> > > > > > > automatically.
> > > > > > > 
> > > > > > > Cheers,
> > > > > > > 
> > > > > > > TIM
> > > > > > > 
> > > > > > > On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:
> > > > > > > > One for Tim, Brad,
> > > > > > > > 
> > > > > > > > What is the status of tophat2 packaging for BL? Google
> > > > > > > > suggests that Brad is working on something. Anything we
> > > > > > > > can do to help?
> > > > > > > > 
> > > > > > > > Thanks,
> > > > > > > > 
> > > > > > > > Will
> > > > > > > > 
> > > > > > > > ---
> > > > > > > > William Spooner
> > > > > > > >                          http://eaglegenomics.com
> > > > > > > > Disclaimer:
> > > > > > > > http://www.eaglegenomics.com/about/privacy-statement/
> > > > > > > > 
> > > > > > > > _______________________________________________
> > > > > > > > Bio-Linux-dev mailing list
> > > > > > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > > > > > 
> > > > > > > -- 
> > > > > > > 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
> > > > > > > -- 
> > > > > > > This message (and any attachments) is for the recipient
> > > > > > > only. NERC
> > > > > > > is subject to the Freedom of Information Act 2000 and the
> > > > > > > contents
> > > > > > > of this email and any reply you make may be disclosed by
> > > > > > > NERC unless
> > > > > > > it is exempt from release under the Act. Any material
> > > > > > > supplied to
> > > > > > > NERC may be stored in an electronic records management
> > > > > > > system.
> > > > > > > _______________________________________________
> > > > > > > Bio-Linux-dev mailing list
> > > > > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > > > > 
> > > > > > ---
> > > > > > William Spooner
> > > > > >                          http://eaglegenomics.com
> > > > > > Disclaimer:
> > > > > > http://www.eaglegenomics.com/about/privacy-statement/
> > > > > > 
> > > > > > _______________________________________________
> > > > > > Bio-Linux-dev mailing list
> > > > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > > > 
> > > > > -- 
> > > > > 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
> > > > > _______________________________________________
> > > > > Bio-Linux-dev mailing list
> > > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > > 
> > > > ---
> > > > William Spooner
> > > >                          http://eaglegenomics.com
> > > > Disclaimer:
> > > > http://www.eaglegenomics.com/about/privacy-statement/
> > > > 
> > > > _______________________________________________
> > > > Bio-Linux-dev mailing list
> > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > 
> > > -- 
> > > 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
> > > _______________________________________________
> > > Bio-Linux-dev mailing list
> > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > 
> > ---
> > William Spooner                          http://eaglegenomics.com
> > Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
> > 
> > _______________________________________________
> > Bio-Linux-dev mailing list
> > Bio-Linux-dev at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > 
> 
> 

-- 
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



More information about the Bio-linux-devel mailing list