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Hi Tim,
<div>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
<a href="http://bowtie-bio.sourceforge.net/index.shtml">http://bowtie-bio.sourceforge.net/index.shtml</a>. 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.</div>
<div><br>
</div>
<div>Am enjoying Biolinux 7 immensely.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Simon<br>
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_________________________________</div>
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Simon Wagstaff<br>
Tel: +44-(0)151-705-3164<br>
Fax: +44-(0)151-705-3371<br>
email: <a href="mailto:simonw@liv.ac.uk">simonw@liv.ac.uk</a><br>
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<div>On 6 Dec 2012, at 21:32, William Spooner wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Thanks Tim,<br>
<br>
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.<br>
<br>
Will<br>
<br>
On 6 Dec 2012, at 18:34, Tim Booth wrote:<br>
<br>
<blockquote type="cite">Hi Will,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Hmmm - they've renamed it from bowtie to bowtie2 so uscan didn't see<br>
</blockquote>
<blockquote type="cite">that the new version was available. I wonder if there's any reason you<br>
</blockquote>
<blockquote type="cite">might want both at once?<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">I'll have a try rebuilding it now.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Cheers,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">TIM<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">On Wed, 2012-12-05 at 22:56 +0000, William Spooner wrote:<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Hi Tim,<br>
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<blockquote type="cite">Many thanks for taking care of this.<br>
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<blockquote type="cite">I've finally got around to trying it out. tophat seems to be the at version 2 (as is cufflinks);<br>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite"><a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/">http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/</a><br>
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<blockquote type="cite">bowtie, however, is languishing on version 0;<br>
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<blockquote type="cite"><a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/">http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/</a><br>
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<blockquote type="cite">Thanks,<br>
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<blockquote type="cite">Will<br>
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<blockquote type="cite">On 14 Nov 2012, at 14:48, Tim Booth wrote:<br>
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<blockquote type="cite">Hi,<br>
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<blockquote type="cite">I've pushed the updates to all these and Velvet, so everything should be<br>
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<blockquote type="cite">Cheers,<br>
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<blockquote type="cite">TIM<br>
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<blockquote type="cite">On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:<br>
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<blockquote type="cite">Many thanks Tim,<br>
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<blockquote type="cite">We'll test that tomorrow. I presume it's the complete bowtie2/tophat2/cufflinks2 stack?<br>
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<blockquote type="cite">Will<br>
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<blockquote type="cite">On 13 Nov 2012, at 16:58, Tim Booth wrote:<br>
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<blockquote type="cite">Hi Will,<br>
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<blockquote type="cite">The TopHat package maintained by Debian Med is up-to-date and seems to<br>
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<blockquote type="cite">build fine on Ubuntu, so I've pushed a newer version to the Bio-Linux<br>
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<blockquote type="cite">PPA. Anyone who already upgraded to BL7 will get the update<br>
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<blockquote type="cite">
<blockquote type="cite">
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<blockquote type="cite">automatically.<br>
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<blockquote type="cite">Cheers,<br>
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<blockquote type="cite">On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:<br>
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<blockquote type="cite">One for Tim, Brad,<br>
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<blockquote type="cite">What is the status of tophat2 packaging for BL? Google suggests that Brad is working on something. Anything we can do to help?<br>
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<blockquote type="cite">Thanks,<br>
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<blockquote type="cite">Will<br>
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<blockquote type="cite">William Spooner <a href="http://eaglegenomics.com">http://eaglegenomics.com</a><br>
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<blockquote type="cite">Disclaimer: <a href="http://www.eaglegenomics.com/about/privacy-statement/">
http://www.eaglegenomics.com/about/privacy-statement/</a><br>
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<blockquote type="cite">_______________________________________________<br>
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<blockquote type="cite">Bio-Linux-dev mailing list<br>
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<blockquote type="cite"><a href="mailto:Bio-Linux-dev@nebclists.nerc.ac.uk">Bio-Linux-dev@nebclists.nerc.ac.uk</a><br>
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<blockquote type="cite"><a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev</a><br>
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<blockquote type="cite">Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
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<blockquote type="cite">NERC Environmental Bioinformatics Centre <br>
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<blockquote type="cite">Maclean Bldg, Benson Lane<br>
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<blockquote type="cite">Crowmarsh Gifford<br>
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<blockquote type="cite">Wallingford, England<br>
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<blockquote type="cite">OX10 8BB <br>
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<blockquote type="cite">This message (and any attachments) is for the recipient only. NERC<br>
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<blockquote type="cite">is subject to the Freedom of Information Act 2000 and the contents<br>
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<blockquote type="cite">it is exempt from release under the Act. Any material supplied to<br>
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<blockquote type="cite">NERC may be stored in an electronic records management system.<br>
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<blockquote type="cite">_______________________________________________<br>
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<blockquote type="cite"><a href="mailto:Bio-Linux-dev@nebclists.nerc.ac.uk">Bio-Linux-dev@nebclists.nerc.ac.uk</a><br>
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<blockquote type="cite"><a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev</a><br>
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<blockquote type="cite">
<blockquote type="cite">---<br>
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<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">William Spooner <a href="http://eaglegenomics.com">http://eaglegenomics.com</a><br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Disclaimer: <a href="http://www.eaglegenomics.com/about/privacy-statement/">
http://www.eaglegenomics.com/about/privacy-statement/</a><br>
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<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
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</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">_______________________________________________<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Bio-Linux-dev mailing list<br>
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<blockquote type="cite">
<blockquote type="cite"><a href="mailto:Bio-Linux-dev@nebclists.nerc.ac.uk">Bio-Linux-dev@nebclists.nerc.ac.uk</a><br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev</a><br>
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<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">-- <br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">NERC Environmental Bioinformatics Centre <br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Centre for Ecology and Hydrology<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Maclean Bldg, Benson Lane<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Crowmarsh Gifford<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Wallingford, England<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">OX10 8BB <br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="http://nebc.nerc.ac.uk">http://nebc.nerc.ac.uk</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">+44 1491 69 2705<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">_______________________________________________<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Bio-Linux-dev mailing list<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="mailto:Bio-Linux-dev@nebclists.nerc.ac.uk">Bio-Linux-dev@nebclists.nerc.ac.uk</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">---<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">William Spooner <a href="http://eaglegenomics.com">http://eaglegenomics.com</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Disclaimer: <a href="http://www.eaglegenomics.com/about/privacy-statement/">
http://www.eaglegenomics.com/about/privacy-statement/</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">_______________________________________________<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Bio-Linux-dev mailing list<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><a href="mailto:Bio-Linux-dev@nebclists.nerc.ac.uk">Bio-Linux-dev@nebclists.nerc.ac.uk</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev</a><br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-- <br>
</blockquote>
<blockquote type="cite">Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
</blockquote>
<blockquote type="cite">NERC Environmental Bioinformatics Centre <br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Centre for Ecology and Hydrology<br>
</blockquote>
<blockquote type="cite">Maclean Bldg, Benson Lane<br>
</blockquote>
<blockquote type="cite">Crowmarsh Gifford<br>
</blockquote>
<blockquote type="cite">Wallingford, England<br>
</blockquote>
<blockquote type="cite">OX10 8BB <br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><a href="http://nebc.nerc.ac.uk">http://nebc.nerc.ac.uk</a><br>
</blockquote>
<blockquote type="cite">+44 1491 69 2705<br>
</blockquote>
<blockquote type="cite">_______________________________________________<br>
</blockquote>
<blockquote type="cite">Bio-Linux-dev mailing list<br>
</blockquote>
<blockquote type="cite"><a href="mailto:Bio-Linux-dev@nebclists.nerc.ac.uk">Bio-Linux-dev@nebclists.nerc.ac.uk</a><br>
</blockquote>
<blockquote type="cite"><a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev</a><br>
</blockquote>
<br>
---<br>
William Spooner <a href="http://eaglegenomics.com">http://eaglegenomics.com</a><br>
Disclaimer: <a href="http://www.eaglegenomics.com/about/privacy-statement/">http://www.eaglegenomics.com/about/privacy-statement/</a><br>
<br>
_______________________________________________<br>
Bio-Linux-dev mailing list<br>
<a href="mailto:Bio-Linux-dev@nebclists.nerc.ac.uk">Bio-Linux-dev@nebclists.nerc.ac.uk</a><br>
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