Support for paired end reads

[brainstorm]

The same way fastq_screen (bowtie -1 -2...) supports. It is not efficient to read the two files sequentially (invoking FACS twice), it should be done at once in one single command.

Thanks @arvestad, @henrikstranneheim and @vals for the input.

[arvestad]

This use case is now also supported by Daniel Lundin. He looked into using facs to screen rRNA, but this was a show-stopper.

[inodb]

Hey! I'll have a look at this for Daniel Lundin if you guys don't have the time to fix this yourself. Any tips on things I should be aware of would be appreciated! I assume there's something tricky about this with the current implementation?

[brainstorm]

Ino, awesome to have you on board to have a look at this issue :D

The implementation itself is a bit tricky, yes, but if you just look at build.c and check.c you should be able to implement paired end support in it.

Feel free to make your own fork and pull request with your changes (code cleanups very welcome as well :)).

[inodb]

Ok, thanks for the tips and the warm welcome!

[arvestad]

I really appreciate it!

Lasse

On 27 Nov 2013, at 10:14, inodb notifications@github.com wrote:

Hey! I'll have a look at this for Daniel Lundin if you guys don't have the time to fix this yourself. Any tips on things I should be aware of would be appreciated! I assume there's something tricky about this with the current implementation?

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[tzcoolman]

I don't have a job now, so I can be supportive as much as possible @inodb

[henrikstranneheim]

Nice to have you onboard Ino.

Cheers,
Henrik
On Nov 27, 2013, at 10:52 AM, inodb notifications@github.com wrote:

Ok, thanks for the tips and the warm welcome!

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Henrik Stranneheim Ph.D.
Department of Molecular Medicine and Surgery
Karolinska Institute
Science for Life Laboratory, KISP
SE-171 65 Solna, Sweden

E-mail: henrik.stranneheim@scilifelab.se
Phone: +46 (0)8 524 81487 (Office)
Phone: +46 (0)736251487 (Mobile)
Visiting address: Tometebodavägen 23A

[dbrami]

Hey folks,
I have no problem with running FACS twice but the issue is if one mate hits a contaminant then its mate should be marked as a contaminant as well. If not, then you are left with asynchronous paired fastq files.
Are there plans to address this as this is a showstopper for pre-assembly filtering.

[arvestad]

It is on our to-do list, but we do not have a time plan for it.

Best,
Lars

On 18 Sep 2014, at 20:15, Daniel Brami notifications@github.com wrote:

Hey folks,
I have no problem with running FACS twice but the issue is if one mate hits a contaminant then its mate should be marked as a contaminant as well. If not, then you are left with asynchronous paired fastq files.
Are there plans to address this as this is a showstopper for pre-assembly filtering.

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