[Bio-linux-dev] tophat2
William Spooner
william.spooner at eaglegenomics.com
Fri Dec 7 04:28:33 EST 2012
Thanks Tim,
Much appreciated, as always!
Will
On 7 Dec 2012, at 09:27, Tim Booth wrote:
> 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
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>>>>>>>> NERC unless
>>>>>>>> it is exempt from release under the Act. Any material
>>>>>>>> supplied to
>>>>>>>> NERC may be stored in an electronic records management
>>>>>>>> system.
>>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>> ---
>>>>>>> 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
> _______________________________________________
> 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/
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