Hi, Not a pressing issue, but I feel like I'm doing this wrong.
Currently in order to get all the reads on a chromosome using Rsamtools (to extract from a BAM file), I'm making an IRanges object that's "as long" as the chromosome I want the reads for. For instance, for chr1: which <- RangesList(chr1=IRanges(start=1, end=247249719)) params <- ScanBamParams(which=which) reads <- scanBam(my.bam.file, param=params)[[1]] Is there are "better" way to do it, eg. w/o making the IRanges object that's stretches over the chromosome? Just curious, thanks. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
