[mira_talk] Re: Quality Clipping
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 23 Jan 2012 19:29:15 +0100
On Jan 23, 2012, at 18:51 , Egon Ozer wrote:
> I think I remember Bastien alluding to this a few months ago, but I thought
> I'd ask since I don't see an easy way to do this in the manual:
> Is it possible to use Mira to just perform quality clipping on Illumina reads
> and output those reads without performing assembly or mapping? Or is there
> an easy way to extract the Mira clipped reads from the assembly/mapping file
> to then use as input for a second assembler?
Yes. Use
-AS:nop=0
then
convert_project -f maf -t ... -c input.maf ...
on the MAF file in the checkpoint directory.
B.
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