[mira_talk] Re: "Simple" assembly: contigs and reads from closing PCRs
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 17 Aug 2011 23:03:09 +0200
On 17 Aug 2011, at 22:34 , Bastien Chevreux wrote:
> Hey! Is that some kind of criticism I read there? If yes, I'm going to sulk
> in the corner :-)
Nope, not at all, but MIRA is very thorough and thus needs time to do things
right... Am I wrong? ;)
> You could either
> a) switch off all clipping routines in MIRA, i.e.
> "--noclipping -CL:pec:no"
Well, I'll try that. But then my closing reads might go wrong, right? I could
then hard clip them before (they are soft clipped in the xml, but I don't know
if -noclipping -CL:pec:no overrides that)
> b) if you do not want to do that, change the data set to look a bit more like
> real sequencing data, see next paragraph on how to do that.
Sounds like a good idea. I gave my reads a quality of 60.
> Depending on the nastiness of your bug, additional measures might be
> necessary in case some of the 5kb overlaps are very similar and MIRA would
> like to join a couple of wrong ones. If that happens: for every 20kb piece
> you add, add the reverse complement sequence. Give the bases of the fwd and
> rev pieces a quality of 45: you don't need to create files for this if your
> PCR product sequences have qualities, then -AS:bdq=45 would give all reads
> without quality a default quality of 45. Then tell the contig object to go on
> a repeat marker base hunt in low coverage, high quality mode:
>
> -CO:mrpg=2:mnq=90:mgqrt=90
>
> This still would not help if there are 100% identical 5kb overlaps in more
> than 2 reads. Never happened to me, but then you would just need to fake SNPs
> in those overlaps to get the assembled correctly.
Mmmh... if I have artificial overlaps of 5kb plus the revcomp strands, that's
then 4 reads with 100% identical overlaps. Thus I would need to fake some SNPs,
right? Makes it a bit complicated...
I'll try with no clipping first.
Thanks for your help!
Lionel
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