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] Martin > > -Kunbin > > > ______________________________________________________________________ > > The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to [email protected] and delete this message, along with any attachments, from your computer. > > _______________________________________________ Bioc-sig-sequencing > mailing list [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
