[mira_talk] Re: Help with MCVc (missing Co Verage in consenus) after mapping assembly
- From: Austen Chen <cyausten@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 17 Feb 2014 20:01:04 +1030
Thank you very much Bastien for your help and suggestions and i will
definitely give it a try and i would like to use new versions of MIRA each
time but it's not something i can do at my fingertip and i need to ask
computer people to do it and it involves a lot of process and that's why....
Austen
On Mon, Feb 17, 2014 at 6:03 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> 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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