[mira_talk] Re: Request for Comments: mirabait for paired-end
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 25 Jun 2014 12:57:04 +0100
On Tue, Jun 24, 2014 at 11:16 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
>> (a) All in one file (using the read names to spot pairs, fine for
>> MIRA input).
>
> I hope you meant “output to one file”. That’s in.
Yes, I mean as output (since MIRA is able to take this as input?).
> If you meant “i have one big unsorted file with pairs and singlets
> mixed” as input … that’s currently not foreseen and I’m not sure
> I want to implement that. There’s one read-naming hell awaiting
> … how to correctly parse out template names if, e.g., Sanger,
> 454 and Illumina are mixed in one FASTQ file?
>
> Any good use case in mind?
This could be useful if your paired data has been through any
non-pair preserving QC or filtering step (e.g. the old mirabait).
But I appreciate this is a complex job, and insisting on nicely
paired input makes sense.
Peter
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