[mira_talk] Re: convert_project -r -v
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 28 Jul 2011 09:52:10 +0200
On Jul 28, 2011, at 9:12 , Nestor Zaburannyi wrote:
> I have tried to use convert_project in order to get rid of the chimeric reads
> at the ends of the contigs, which prevent further contig-joining.
Are you sure that those reads are chimeric? I ask because MIRA has become quite
good at filtering them out and they should appear in contigs only very, very
rarely nowadays.
> I use:
> convert_project -f maf -t fasta -r c -v 2 infile.maf outfile.fasta
> but the contigs remain the same, I still have stretches on the ends with
> coverage = 1. Why these are not converted to N's? Can MIRA filter out regions
> with coverage=n during assembly? Any trick/switch?
Hmmmm ... I haven't used "-v" in a long time, I have to look whether some
recent changes to the consensus machinery have made it loose its function.
B.
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