[mira_talk] Re: convert_project -r -v
- From: Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>
- To: Bastien Chevreux <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 28 Jul 2011 10:03:25 +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 am pretty sure. Most of the time, bases that are "out of alignment" and with
coverage=1 at the end of one contig can be mapped in the middle of other
contigs.
>> 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.
Please, do.
Sincerely yours
Nestor
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