[mira_talk] Re: Filtering out crappy sequence
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 4 Apr 2012 20:27:16 +0100
On Wed, Apr 4, 2012 at 8:09 PM, John Nash <john.he.nash@xxxxxxxxx> wrote:
> 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
What were the failing sequences? Perhaps there is something we
can suggest after seeing them and in what way they are bad.
Peter
--
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:
