[khmer] khmer/khmer-protocols confusion

[Michael R. Crusoe]

On Mon, Feb 24, 2014 at 12:22 PM, Francesco Rubino [frr11] <frr11 at aber.ac.uk
> wrote:

>  Hi Michael,
>
>
>  thanks for your reply. I wasn't sure about the version because I did
> find some documentation online about version 0.8.x and I got confused.
> Regarding the casava format, this is the page:
> http://khmer.readthedocs.org/en/latest/scripts.html
>
> In the section about read handling it mention the format @name/1 as the
> latest.
>

Thanks. I've updated this in the documentation for the newly released v0.8
of the khmer project.


>
>  Should I change my files to be interleaved and with the headers in the
> old format (the one ending in /1 or /2) to make sure I
>
> don't run into problems in some of khmer scripts?
>

Correct. If you want your reads processed as pairs you need to use the
/1,/2 format for now.


>
>  I have code to interleave and detect the and convert the header format
> anyway, so it won't really be a problem, but I'd prefer not to if possible.
>

Sorry, this is on our roadmap to fix this issue.


>
>  Thanks,
>  Francesco
>
> ------------------------------
> *From:* Michael R. Crusoe <mcrusoe at msu.edu>
> *Sent:* 24 February 2014 17:07
> *To:* Francesco Rubino [frr11]
> *Cc:* khmer at lists.idyll.org
> *Subject:* Re: [khmer] khmer/khmer-protocols confusion
>
>
>
> On Mon, Feb 24, 2014 at 10:58 AM, Francesco Rubino [frr11] <
> frr11 at aber.ac.uk> wrote:
>
>>  Hello all,
>>
>
>  Hello Francesco,
>
>  Thank you for using the khmer suite and for your questions.
>
>
>>  I've read part of the documentation of khmer and I'm interested in
>> using it to either partition or normalise a meta-transcriptome I have. I
>> have a bit of confusion about the versions of the software, though. I have
>> a few questions I hope you can answer:
>>
>>  1) I've read both about a khmer 0.7.x (
>> http://khmer.readthedocs.org/en/latest/) and a 0.8.x (
>> https://github.com/ctb/khmer/releases). Which should I use?
>>
>
>  The official GitHub repository for khmer is
> https://github.com/ged-lab/khmer. The latest current release is v0.7.1.
> Our primary method for distribution is via the Python Package Index (
> https://pypi.python.org/pypi/khmer ) using the `pip` command as
> documented in http://khmer.readthedocs.org/en/latest/
>
>  GitHub will present any branch or tag as a release. Titus's personal
> repository has a branch named "protocols-v0.8.3" in reference to the
> version of khmer-protocols not of the khmer project itself.
>
>
>>   2) I see in the documentation that you need to interleave the fastq
>> files if using paired-end data. Why do you refer as "@name/1" as the new
>> casava format? I thought that one is the old one.
>>
>
>  That would be our error. Supporting the new format is being tracked in
> this GitHub issue: https://github.com/ged-lab/khmer/issues/23
>
>  What document where you looking at?
>
>
>>
>>  Thanks,
>>  Francesco Rubino
>>
>> _______________________________________________
>> khmer mailing list
>> khmer at lists.idyll.org
>> http://lists.idyll.org/listinfo/khmer
>>
>>
>
>
>  --
> Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
>  @ the Genomics, Evolution, and Development lab; Michigan State U
> http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe<http://twitter.com/biocrusoe>
>



-- 
Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
 @ the Genomics, Evolution, and Development lab; Michigan State U
http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670
@biocrusoe<http://twitter.com/biocrusoe>
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