dear all: sorry to disturb you ,especially martin. but i feel so confused, when i use alnRanges <- readBamGappedAlignments("s_5_1-IS_sequence.bam",format="BAM") it wored well but when i use paraFlag <- scanBamFlag(hasUnmappedMate = T) para <-ScanBamParam(flag = paraFlag) alnRanges <- readBamGappedAlignments("s_5_1-IS_sequence.bam",format="BAM",which=par a) it reported error Error in open.BamFile(BamFile(file, index), "rb") : failed to load BAM index file: /home/sgao/Algae_data/s_5_1-IS_sequence.bam In addition: Warning message: In open.BamFile(BamFile(file, index), "rb") : [bam_index_load] fail to load BAM index. > sessionInfo() R version 2.13.2 (2011-09-30) Platform: x86_64-unknown-linux-gnu (64-bit) 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] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-33 [4] Biostrings_2.20.4 GenomicRanges_1.4.8 IRanges_1.10.6 loaded via a namespace (and not attached): [1] Biobase_2.12.2 grid_2.13.2 hwriter_1.3 [[alternative HTML version deleted]]

On 11/02/2011 03:15 PM, wang peter wrote: > dear all: > sorry to disturb you ,especially martin. > but i feel so confused, when i use > alnRanges<- readBamGappedAlignments("s_5_1-IS_sequence.bam",format="BAM") > it wored well > but when i use > paraFlag<- scanBamFlag(hasUnmappedMate = T) > para<-ScanBamParam(flag = paraFlag) > alnRanges<- > readBamGappedAlignments("s_5_1-IS_sequence.bam",format="BAM",which=p ara) > > it reported error > > Error in open.BamFile(BamFile(file, index), "rb") : > failed to load BAM index > file: /home/sgao/Algae_data/s_5_1-IS_sequence.bam > In addition: Warning message: > In open.BamFile(BamFile(file, index), "rb") : > [bam_index_load] fail to load BAM index. > use idx = indexBam("s_5_1-IS_sequence.bam") to create an index. If your bam index file is not named following samtools convention (e.g., with extension '.index'), specify it separately bf = open(BamFile("s_5_1-IS_sequence.bam", "s_5_1-IS_sequence.index")) readBamGappedAlignments(bf) An index is required to access portions of a bam file. In R-2-13.2, readBamGappedAlignments only accepts GRanges as 'which'; to use ScanBamParam needs R-2-14.0 and Rsamtools 1.6.0. Martin > >> sessionInfo() > R version 2.13.2 (2011-09-30) > Platform: x86_64-unknown-linux-gnu (64-bit) > 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] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-33 > [4] Biostrings_2.20.4 GenomicRanges_1.4.8 IRanges_1.10.6 > loaded via a namespace (and not attached): > [1] Biobase_2.12.2 grid_2.13.2 hwriter_1.3 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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: M1-B861 Telephone: 206 667-2793