[mira_talk] Filtering out crappy sequence
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 4 Apr 2012 15:09:50 -0400
Dear mira users,
I just received some sff files from our sequence facility, so dutifully, I ran
sff_extract and produced a nice fastq / xml file set ready for MIRA.
MIRA crashed with a "Sanity check of read '<insert read name here>' failed"
error. I went and looked at the failed sequence and sure enough, it was crap.
So I fired up emacs and removed the offending entry, and yes, it happened again.
I don't particularly want to remove bad sequences using the "fail by crashing
mira" followed by "edit using emacs" approach. Before I go and try and write
code to examine and filter out bad fastq data, is there something obvious out
there that I could use?
Thanks
John
--
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:
