On 02/18/2010 06:58 AM, Ramzi TEMANNI wrote: > Hi, > I'm encountering the following error when trying to load fastq file: > > Error in .local(dirPath, pattern, ...) : > _DNAencode(): key 73 not in lookup table
Your fastq file is not conforming to readFastq's expectations, probably reading say a quality string or identifier and thinking it should be reading a DNA sequence. Maybe there's a missing carriage return or other problem? Also, readFastq handles files as specified in ?readFastq and in particular expects a fastq record to consist of exactly four lines. If fastq files in a different format are being produced, then I'll take the opportunity to update ShortRead. Martin > > Key 73 in ascii table is "I" (capital i) > > Anyone had encountered such error before ? > > Thanks in advance for your help > > Regards, > Ramzi > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.2.0 ShortRead_1.4.0 lattice_0.18-3 > BSgenome_1.14.2 > [5] Biostrings_2.14.12 IRanges_1.4.11 > > loaded via a namespace (and not attached): > [1] Biobase_2.6.1 grid_2.10.1 hwriter_1.1 RCurl_1.3-1 XML_2.6-0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
