Hello, all; is there no qa() function in ShortRead for BAM files? I've noticed there is no BAM-specific qa function in the documentation for ShortRead. I've imported a BAM representing a single lane on a Illumina IIGA run after alignment with Bowtie and conversion of SAM to BAM with samtools thus: params <- ScanBamParam(scanBamFlag(isUnmappedQuery=FALSE), what=scanBamWhat()) lane1 <- readAligned("s_1_sequence.txt.sorted.bam.bam", type="BAM", param=params) which reads in ok, but qa complains: qa(lane1) Error: UserArgumentMismatch 'lane' must be 'character(1)' Is this because there is no function to handle BAM files? Or is this some problem with the file itself or with only using a single read? For what it's worth, coverage runs fine on this object. Hollis Wright, PhD Oregon Clinical and Translational Research Institute

On 10/06/2010 12:55 PM, Hollis Wright wrote: > Hello, all; is there no qa() function in ShortRead for BAM files? I've noticed there is no BAM-specific qa function in the documentation for ShortRead. I've imported a BAM representing a single lane on a Illumina IIGA run after alignment with Bowtie and conversion of SAM to BAM with samtools thus: > > > params <- ScanBamParam(scanBamFlag(isUnmappedQuery=FALSE), what=scanBamWhat()) > lane1 <- readAligned("s_1_sequence.txt.sorted.bam.bam", type="BAM", param=params) > > which reads in ok, but qa complains: > > qa(lane1) > Error: UserArgumentMismatch > 'lane' must be 'character(1)' > > Is this because there is no function to handle BAM files? Or is this some problem with the file itself or with only using a single read? For what it's worth, coverage runs fine on this object. Hi Hollis, No, qa() wants to identify the samples it's doing qa on, so it's looking for qa(lane1, "IAmNumberOne") The documentation can be found, awkwardly, by looking for the qa method that is being used selectMethod(qa, class(lane1)) which leads to a lot of output and then Signatures: dirPath target "AlignedRead" defined "ShortReadQ" and then the help page for the 'defined' class, > ?"qa,ShortReadQ-method" FWIW, there is also an rbind defined, so rbind(qa1, qa2, <...>) where the qa1, qa2, etc might have been generated by sequential calls to readAligned, i.e., only ever having one set of reads present in memory at a time (the size of the results of qa() are small). Also, There will be a qa method for BAM files in the forthcoming release. And we'll try to make the documentation more accessible on this point. Martin > > Hollis Wright, PhD > Oregon Clinical and Translational Research Institute > _______________________________________________ > 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