[mira_talk] Re: assembly runs out of temp space

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.


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