On 11/30/2012 08:06 AM, Maria Dermit wrote: > Dear list, > > I am trying to read with some aligmnets files generated wiht Bowtie2 with > readAligned function of ShortRead package with this code: > > readAligned("SRR030012.sra.1.aln.short.aln",type="Bowtie") > > and I get this error: > > error: unable to find an inherited method for function "strand", for > signature "AlignedRead" > > I attach here the first 10 lines of one of my alignment files. Hi Maria -- readAligned type="Bowtie" was introduced to read a format produced by earlier versions of Bowtie. My recommendation is that you arrange for Bowtie2 to generate BAM files, and then use Rsamtools::readBamGappedAlignments (which allow for more flexible input, and represents the data in the 'GenomicRanges' way. Your packages are a mixture of 'release' and 'devel' versions, and I think also from different releases; you should source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") It's a bit hard to see how 'strand' wouldn't be available after library(ShortRead); I see > showMethods(strand) Function: strand (package BiocGenerics) x="AlignedRead" ... But I'm happy to investigate further if the problem persists. The attachment didn't get through the email, can you forward it to me privately? Martin > > Many thanks for your help. > > Kind Regards, > > Maria > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.12.4 latticeExtra_0.6-24 RColorBrewer_1.0-5 > [4] Rsamtools_1.9.30 lattice_0.20-10 Biostrings_2.25.12 > [7] GenomicRanges_1.9.59 IRanges_1.15.42 BiocGenerics_0.3.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.25.7 > [4] grid_2.15.0 hwriter_1.3 RCurl_1.95-1.1 > [7] rtracklayer_1.17.19 stats4_2.15.0 tools_2.15.0 > [10] XML_3.95-0.1 zlibbioc_1.4.0 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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