[mira_talk] Re: assembly runs out of temp space
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 26 Apr 2012 22:26:54 +0200
On Apr 26, 2012, at 18:58 , Adam Witney wrote:
> Not done it quite the way you suggested, but I have used Heng Li's tool seqtk
> to trim reads over 100 bases based on quality scores. (It was already
> available and saved me writing something new). Tool is here for anyone
> interested
There's nothing bad in not re-inventing the wheel :-)
> This seems to have led to an improvement and mira completed the assembly
> without running out of disk space. Here are the stats before and after
> trimming:
After trimming looks way better, both in FASTQC and in MIRA. Still not
brilliant, there are artefacts remaining, but obviously better.
>> If 1&2 gave "better" results, ask your sequencing provider why on earth they
>> gave you unclipped junk sequences.
>
> I would but its our own machine! :-) This data was straight off the machine!
> We now have to figure out why the sequencing didn't work out so well.. the
> 200bp kits don't seem to work as well at as the 100bp kits yet (in our hands).
Oooops :-) Maybe you then should ask Life why their software did not trim
correctly.
> Thanks again for your help Bastian
Happy to help,
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:
