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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