[mira_talk] Re: Extracting reads from a mapping asembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 20 May 2014 20:23:32 +0200
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.
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
