[Bio-linux-dev] tophat2

[Wagstaff, Simon]

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:Bio-Linux-dev at nebclists.nerc.ac.uk>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20121206/b596f9c9/attachment.html>