[Bioc-sig-seq] short read low complexity filtering

Hervé Pagès hpages at fhcrc.org
Thu Dec 9 00:10:43 CET 2010

On 12/08/2010 03:03 PM, Hervé Pagès wrote:
>> Also, how would we generate the two output files:
>> name_low_complexity_removed.fastq and low_complexity_reads.fastq?
> You could try to use write.XStringSet(... , format="fastq") for this.
> Or use the IO facilities of the ShortRead package. It depends what you
> want to do with the scores.
I meant "with the qualities". The FASTQ format stores the qualities of
the reads too.


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