Hi Adrian,
Thanks for the email.
We did a pass filtering at Q=33, if I remember correctly. Though we have
not done any 3' trimming.
I'm retrying with k=21 and if that still appears to have problems, I'll
attempt again with a higher quality thresh hold and some 3' trimming.
Though I'll have to look into just how much trimming is typical, do you
have any suggestions?
Walter
2011/7/20 Adrian Platts <[email protected]>
> >
> > That is the first thing you should do I think. k=21 will pick up more
> redundant k-mers than k=31 or k=61.
> >
> > Basically, this is why:
> >
> >
> > If the sequencing error rate is > 4.7% (1/21), then mostly all k-mers
> will be unique and bad for k=21.
> > If the sequencing error rate is > 3.2% (1/31), then mostly all k-mers
> will be unique and bad for k=31.
> > If the sequencing error rate is > 1.6% (1/61), then mostly all k-mers
> will be unique and bad for k=61.
> >
> > I believe Illumina HiSeq TruSeq sequencing error rate varies between 0
> and 2 %. You mileage may vary however depending on the quality of DNA and
> library preparation (nicks
> > in DNA for instance during the library preparation).
> >
>
> I believe that most people using long Kmers in assembly have been 3'
> trimming/rejecting reads where they fall below (at least) Q=31 on a per read
> basis and
> with the newer Illumina chemistries at Q=35. I don't know of anyone who is
> really putting raw FASTA read data directly into the assemblers - certainly
> not when using long Kmers
> for exactly the reason above.
>
> I suppose FASTQ data perhaps but the way the FASTQ data is dealt with can
> be pretty different between assemblers so it can have mixed results I think.
>
> Adrian
>
>
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