[Bioc-sig-seq] readFastq

Martin Morgan mtmorgan at fhcrc.org
Sat Oct 16 00:27:51 CEST 2010

On 10/15/2010 02:42 PM, Kunbin Qu wrote:
> Dear all,
> I have a fastq file with reads having variable length of adapters. I
> have trimmed them with trimLRPatterns. Some of them was shortened to
> 0 bp. I would like to draw a histogram on the trimmed reads, but when
> I used readFastq, it crashed out when it encountered the reads with 0
> bp. Is there a way to get around? Thanks.

I suspect this is a bug in ShortRead's parsing of fastq files. Maybe
filter the zero-width trimmed reads before writing them to disk?

   fq = fq[width(fq) != 0]


> -Kunbin
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