[mira_talk] Re: Doubts
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 8 Oct 2014 13:24:35 +0200 (CEST)
> On October 8, 2014 at 9:00 AM Bobby Paul <bobbypaul29@xxxxxxxxx> wrote:
> I have assembled (de novo) the bacterial (Burkholderia pseudomallei) genome
>using MIRA 4.0.2 and I got 1845 contigs.
> Sorry for the disturbance, I referred in MIRA free lists but not get the
>proper answer for following queries. Expecting your valuable suggestions on
>below given queries.
> 1. Is there any parameter to reduce number of contigs and get larger
>contigs.
There is no "magic" parameter for this kind of thing, no. I suspect your data
set has in interesting ... "challenge" somewhere.
> 2. Is there any way to get only the unaligned/unmapped reads from fastq
>file after de novo and reference based assemblies.
Yes. Use "miraconvert" in conjunction with information you can extract from the
debris files.
> 3. How to calculate the percentage of unmapped regions or region where
>less than 10 reads aligned from reference assembly with respect to the total
>genome.
For regions without any coverage in a mapping assembly: these are annotated with
a MCVc tag. See the consensustaglist in the info directory. As to regions with
less than 10 reads: the routines for this are present in MIRA, but currently not
integrated into miraconvert. So atm there's no easy way to get that information.
Maybe there are tools which do that for SAM/BAM?
> 4. How to calculate the percentage of unique reads aligned in both
>reference and de novo assembly as well as reads aligned 2 times 3 times etc.
In MIRA, each read is aligned only once.
B.
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