[mira_talk] Re: Using paired-end sanger data
- From: Saravanaraj Ayyampalayam <raj@xxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 29 Sep 2009 15:32:42 -0400
Thanks everybody.
I will try re-naming the reads with the f and r naming scheme.
This data was generated in our university genome center and use their
own naming system.
Thanks.
-Raj
Chris Taylor wrote:
Raj, the "fr" is what I have done in the past. You should see in the
log whether MIRA recognizes the mate.
On Tue, Sep 29, 2009 at 12:54 PM, Bastien Chevreux <bach@xxxxxxxxxxxx
<mailto:bach@xxxxxxxxxxxx>> wrote:
On Dienstag 29 September 2009 Lionel Guy wrote:
> You need to indicate them in the .xml file that contains
clipping and
> paired-end data (like the NCBI traceinfo file). There is an
example in
> the mira folder, in minidemo/data/bbdataset1/
> cjejuni_demo_in.sanger.xml. The important fields for paired-end data
> are insert_stdev, insert_size, template_id and trace_end. To have a
> more minimalistic example, have a look at this:
There is actually a simpler way IF AND ONLY IF you are using one
library size:
set the minimum insert size in MIRA via
"-GE:tismin=...:tismax=..." and then
tell MIRA the read naming scheme via -LR:rns=...
> The paired-end reads are already named with .b1 and .g1 to
indicate pairs.
> e.g. >aspbac55b1_1_A01_C001.b1 and >aspbac55b1_1_A01_C001.g1
That's a problem ... I don't recognize the naming scheme. It's not
from the
Sanger Centre, TIGR, St.Louis ... or is it?
If everything else fails: rename the reads quickly, replacing the
"b" by a "f"
and the "g" by a "r" and then use the forward/reverse naming
scheme of MIRA.
Ie.:
>aspbac55b1_1_A01_C001.f1
and
>aspbac55b1_1_A01_C001.r1
and "-LR:rns=fr"
That should do the trick.
Regards,
Bastien
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