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. 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