[mira_talk] Re: Settings for ddRAD data using EST mode
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 8 Oct 2014 21:58:39 +0200
On 08 Oct 2014, at 18:01 , Magnus Popp <magnus.popp@xxxxxxxxxx> wrote:
> Concerning your examples below, I’m OK with the first case as I would
> interpret an IUPAC "R" as a result of merging what probably are two alleles,
> but ideally mira would give me two contigs. I see that wasn’t what I wrote in
> my question, but that’s what I meant, sorry…
Here again, MIRA will give you two contigs if there is enough evidence for each
base. Getting IUPAC bases means: there was not enough evidence to discard a
sequencing error as possibility, but there is too much evidence to make make a
clean base call.
> In second example the preferred result would be that the contig (or perhaps
> the read) is clipped when the quality drops that low.
>
> I will align each RAD loci/“EST” across a handfull of fairly closely related
> species and although the errors (be it a single base or a IUPAC base) most of
> the time only will result in apomorphic characters, they will mess up the
> diversity and branch length estimates in my phylogenetic analyses. So I
> rather have somewhat shorter RAD loci/ESTs with ± reliable data than longer
> ones with shaky 3’ ends at this stage.
If push comes to shove, use the option to force non-IUPAC base calling:
-CO:fnicpst Well, forcing may be a bit too much said: it will reduce the
IUPACs.
> Unless you suggest otherwise, I’ll probably use miraconvert and set -q to
> something that works with my data and then simply truncate at the first N or
> perhaps just merge the fasta and qual files and use a suitable cut off in
> fastq quality trimmer.
Well, I just looked up the code and found the reason why I deactivated it: a
class in command line parameters. It used to be “-v”, but I since moved the
version output to this. I simply forgot to reassign a new parameter. “-V” seems
to be free … I’ll have a look whether I can give you a snapshot of the dev tree
later-on this week.
B.
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