[mira_talk] Re: Getting observed insert size etc for paired end reads
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 13 Feb 2014 09:48:50 +0000
On Wed, Feb 12, 2014 at 9:38 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> 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.
Great - thanks Bastien.
I'm doing this with grep:
$ grep ^ATG -A 3 assembly.log
ATG PREDICTIONS
rgid: 1 c: 161712 sp: -2 m: 113.6219227891 d:
31.3431858333 s: -0.1626077222 -: 50 +: 176
rgid: 1 c: 620869 sp: -1 m: 244.2576642220 d:
123.1716308278 s: 0.7693070253 -: 22 +: 515
Final prediction: rgid: 1 c: 620869 sp: -1 m: 244.2576642220
d: 123.1716308278 s: 0.7693070253 -: 22 +: 515
--
ATG PREDICTIONS
rgid: 1 c: 161180 sp: -2 m: 111.8964201514 d:
30.8984276809 s: -0.1555124536 -: 50 +: 173
rgid: 1 c: 613365 sp: -1 m: 231.4318040621 d:
114.9710732224 s: 0.7802482977 -: 24 +: 484
Final prediction: rgid: 1 c: 613365 sp: -1 m: 231.4318040621
d: 114.9710732224 s: 0.7802482977 -: 24 +: 484
--
ATG PREDICTIONS
rgid: 1 c: 160397 sp: -2 m: 111.2749847255 d:
30.7681223973 s: -0.1499654587 -: 49 +: 172
rgid: 1 c: 610365 sp: -1 m: 230.1019698574 d:
114.2280587811 s: 0.7776165138 -: 24 +: 481
Final prediction: rgid: 1 c: 610365 sp: -1 m: 230.1019698574
d: 114.2280587811 s: 0.7776165138 -: 24 +: 481
--
ATG PREDICTIONS
rgid: 1 c: 159008 sp: -2 m: 111.2163714004 d:
30.7810822718 s: -0.1497065318 -: 49 +: 172
rgid: 1 c: 604403 sp: -1 m: 229.8911552540 d:
114.0643954342 s: 0.7746355633 -: 24 +: 480
Final prediction: rgid: 1 c: 604403 sp: -1 m: 229.8911552540
d: 114.0643954342 s: 0.7746355633 -: 24 +: 480
--
ATG PREDICTIONS
rgid: 1 c: 159089 sp: -2 m: 111.3048965994 d:
30.6778592767 s: -0.1515380996 -: 49 +: 172
rgid: 1 c: 608715 sp: -1 m: 229.7921947666 d:
113.9986506361 s: 0.7775140932 -: 24 +: 480
Final prediction: rgid: 1 c: 608715 sp: -1 m: 229.7921947666
d: 113.9986506361 s: 0.7775140932 -: 24 +: 480
Those are the predictions for each of the five passes - settling down to a mean
template size of approx 230, standard deviation 114, skew 0.77, min 24, max 480.
However, the MAF header seems to have the min/max from the first pass (22, 515),
is that an error?
@ReadGroup
@RG name MiSeq
@RG ID 1
@RG technology Solexa
@RG strainname StrainX
@RG templatesize 22 515
@RG segmentplacement FR
@RG segmentnaming solexa
@EndReadGroup
Thanks,
Peter
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