Hi, I'm trying to work with *.bam and *.bai files produced using Bioscope (SOLiD related software package, v.1.2.1). I tried two examples in the Rsamtools manual (the one on top of the page 2 for querying the reads in the given range, and the one on the bottom of the page 4 for calculating coverages for chunks of the file). I tried with files of different sizes (35Mb, 1.8Gb) but the code in both examples just kept running without any error messages and without producing results in any reasonable time. I even left it running over night but it still hadn't finished. My computer has Mac OS X 10.6.4 with 8Gb memory. The session info is attached below. Are there any known issues with Rsamtools and bam/bai files originating from SOLiD Bioscope software? Many thanks for all advice in advance, Asta sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rsamtools_1.0.8 Biostrings_2.16.9 GenomicRanges_1.0.7 [4] IRanges_1.6.11 loaded via a namespace (and not attached): [1] Biobase_2.8.0

On 10/12/2010 12:27 AM, Asta Laiho wrote: > Hi, > > I'm trying to work with *.bam and *.bai files produced using Bioscope (SOLiD related software package, v.1.2.1). I tried two examples in the Rsamtools manual (the one on top of the page 2 for querying the reads in the given range, and the one on the bottom of the page 4 for calculating coverages for chunks of the file). I tried with files of different sizes (35Mb, 1.8Gb) but the code in both examples just kept running without any error messages and without producing results in any reasonable time. I even left it running over night but it still hadn't finished. My computer has Mac OS X 10.6.4 with 8Gb memory. The session info is attached below. Are there any known issues with Rsamtools and bam/bai files originating from SOLiD Bioscope software? > > Many thanks for all advice in advance, Hi Asta -- I don't know of outstanding issues. If the query is expected to retrieve a 'small' number of reads (millions, say) then it should be fast (as in not enough time to check your email). If it's returning large numbers of reads then memory might become a problem. If there is a 'bug' my guess would be that it involved integer overflow in the index -- seeking a read that is late in a very large BAM file. So... verify basic functionality with library(Rsamtools); example(scanBam) try accessing a few reads at the beginning of the first reference sequence returned by scanBamHeader(fl)[[1]][["targets"]] where 'fl' is the name of your BAM file. If this doesn't provide any hint then please include a minimal script sufficient to reproduce your problem. It would be very helpful to point to a publicly available BAM file generated by the same tools as you are using. Martin > Asta > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Rsamtools_1.0.8 Biostrings_2.16.9 GenomicRanges_1.0.7 > [4] IRanges_1.6.11 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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: M1-B861 Telephone: 206 667-2793