[BioC] readAligned with bowtie2 input
Maria Dermit
maria.dermit01 at gmail.com
Fri Nov 30 17:06:09 CET 2012
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
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