[mira_talk] Re: Extracting reads from a mapping asembly
- From: Chayan Roy <chayan.roy93@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 21 May 2014 00:50:24 +0530
Thanks to both of you for your suggestions...well the option 2a sounds easy
to me and I will start wit that one..thanks again
On Tue, May 20, 2014 at 11:53 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
> On 20 May 2014, at 7:23 , Chayan Roy <chayan.roy93@xxxxxxxxx> wrote:
> > I have performed a mapping assembly with unpaired iotorrent reads. After
> the assembly I tried to extract the reads but not the contigs (or the
> consensus) with
> > "miraconvert -f caf -t fastq -M sourcefile.caf file.fastq"
> > but along with the reads it also extracted the contigs as well which is
> creating problem when i tried to perform a denovo with the extracted reads.
>
> miraconvert did not extract the contigs, but it extracted the backbone
> reads which were given by the reference sequences you took for the backbone
> assembly. Which is the intended behaviour :-)
>
> There is unfortunately no single miraconvert option for what you want, but
> there are different possibilities to still reach your goal with little
> hassle:
>
> 1. As Chris pointed out, there is an info file which gives you all read
> names for all contigs. Using some basic processing commands (grep and cut),
> you quickly get a list you can use with the -n option of miraconvert.
>
> OR
>
> 2a. Continuing with what you have (a file with mapped reads and reference
> reads): well, you know the name of the reference reads, right? You can use
> miraconvert -n -i to get them out.
>
> OR
>
> 2b. Continuing with what you have (a file with mapped reads and reference
> reads): well, you know the name of all the reads you tried to map, right?
> You can use miraconvert -n to get just these.
>
>
> Hope that helps,
> B.
>
>
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--
*CHAYAN ROY*
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