[mira_talk] Re: Getting observed insert size etc for paired end reads
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 12 Feb 2014 22:38:31 +0100
On 12 Feb 2014, at 19:15 , Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
> For paired end libraries, does MIRA report any of the observed
> template/insert size, orientation, fraction assembled in same
> contig, or something like the SAM FLAG for "properly mapped"
> somewhere?
That’s something where proper output did not make it into 4.0. There are ways
to extract all that info (except fraction) from the output log, but they’re
tedious and the format will change. If you want to give it a try anyway, grep
for “^ATG” in the log. You’ll see reports (mean, stdev, skewdness, inferred
min/max) for every readgroup. Pass 1 does not count, look in pass 2 and there
for the final predictions.
If you are just interested in min/max of the templates, look at the header of
the MAF files (results or, during assembly, checkpoint).
B.
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