a simple range of the numerical quality values should usually suffice to
guess the Illumina/Sanger scale. Sanger is 1 to 40, Solexa is -5 to
60(?). In any case, if you have negative values you're dealing with a
Solexa fastq file.
Vincent Carey wrote:
thanks to both Martin and Cei -- clearly I have to have the scale right,
and it is my hope to do a bit of analysis of the quality score distributions
and of decisionmaking using these -- positional effects are clearly of
interest.
On Wed, Apr 15, 2009 at 6:25 PM, Cei Abreu-Goodger <[email protected]
<mailto:[email protected]>> wrote:
Hi Vincent,
Are you taking into account that quality scores will tend to drop
off towards the end of the run? I would probably restrict any sort
of quality filtering to the first x bases of each read... From my
experience, only a very small fraction of reads out of a "good" run
would be removed due to general quality issues. Also, if your
further pipeline is "quality-aware" (eg MAQ/bowtie for alignments)
you can get away with not worrying initially about the quality of
the reads. On the other hand, for some kinds of analysis I was
dropping the quality scores and making plain fasta files. In these
cases it would pay off to convert very low-quality bases to Ns,
since I would get better coverage.
Cheers,
Cei
Vincent Carey wrote:
i have scoured our archives and found little regarding role of
solexa
quality
scores as reported in fastq outputs in short read filtering.
my understanding is that a numerical score of -4 or greater
indicates more
probability
mass on the called base than on any other. in checking 1e6
reads on each of
two lanes
i found the frequency of the event " fewer than three bases have
score less
than -4" to be
4e-3 in one lane and 2e-3 in another. in other words, filtering by
requiring no more than
two < -4 scores would take you from a million reads to about
2000-4000,
assuming i have
not taken a biased sample (i may have, just took the first 1e6
in fastq).
is there any reason to regard a call with score < -4 to be much
different
from an 'N'?
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Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265
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The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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