[mira_talk] Re: Help with MCVc (missing Co Verage in consenus) after mapping assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 17 Feb 2014 08:33:40 +0100
On 17 Feb 2014, at 5:27 , Austen Chen <cyausten@xxxxxxxxx> wrote:
> […] however I have instead used convert_project
Using an older version of MIRA? That program has been renamed “miraconvert” and
remember that the SAM output contains some fixes, too.
> Also i want to know if the reference has regions that are missing but not in
> my strains and i seem to unable to find this piece of information (after
> comparing 6 strains to the same reference).
This is not something which a simple mapping can tell you right away. However,
getting that kind of information is quite trivial. For each of your strain, do
the following:
1. Extract all the unmapped reads into a new FASTQ. Use miraconvert /
convert_project with the -n option, giving it the debris info file for that.
2. Assemble de-novo the reads in this new FASTQ. I recommend that you assemble
these reads not in “genome” mode but in “est” mode.
3. Analyse the resulting contigs: those not being joins of your mapped strains
(compared with the reference) and having an average coverage of >=75% of the
average coverage of the mapping are something you are looking for. Basically,
every contig with more than a couple of hundred bases (if using Illumina) is
almost a sure hit.
B.
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