[mira_talk] How to disable right end base masking for solexa data in mira.
- From: Markiyan Samborskyy <ms587@xxxxxxxxxxxxxxxxxx>
- To: Bastien Chevreux <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 10 May 2012 19:23:15 +0100
Dear Bastien,
Is there a way of disabling the masking (conversion to the n) of the
first base in every solexa read (miseq), other then telling MIRA that
they come from 454?
The reads are preprocessed by my fastq import/filter tool and have all
detectable
crap removed/clipped, so only good sequence should remain.
I've tried setting the following parameters:
-CL:cbse=no
-CL:c3pp=no:ckar=no
But it still changes the first base in every read to n, and sets
quality to 0. And as a results all reads in the resulting ace file doesn't
match the phd.ball files, and the consed (v22) is complaing... (and
doesn't show any read quality data).
The reads were saved in the *.fasta, *.fasta.qual and *.xml files
before inputing into the mira.
--
Best regards,
Markiyan mailto:ms587@xxxxxxxxxxxxxxxxxx
--
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:
