Hi Karl, On Wed, Jan 27, 2010 at 5:00 PM, Dykema, Karl <[email protected]> wrote: > Hi all, > > We have been using Rsamtools to import BAM files also. On previous sequencing > runs the BAM files were around 800 megs and I could import the entire BAM > with .readAligned_bam(). Our new sequencing data creates larger BAM files and > I am unable to import them like before. So, as Steve pointed out to me > offline, I probably will need to import the reads from each chromosome > individually. Unfortunately it does not seem to be recognizing my chromosome > names, error msg below. Has anyone had a similar problem or recognize > something that I might be doing incorrectly? Thanks in advance. > > >> which <- RangesList(chr1=IRanges(start=1,end=247249719)) >> params <- ScanBamParam(which=which) >> >> chr1reads <- scanBam("../aln.sorted.nodupes.bam",param=params) > Error in function (bam, tmpl, space, start, end) : failed to scan BAM > file: � > last record: 0 > In addition: Warning message: > In function (bam, tmpl, space, start, end) : 'space' not in BAM header > file: ../aln.sorted.nodupes.bam > space: chr1
Perhaps the chromosome names are different in your BAM file. I think you can list them using samtools, like so (from the command line): $ samtools view -H aln.sorted.nodupes.bam You should get a lot of lines that start with @SQ -- the names of "the spaces" are there, some of the output from one of my files looks like: @SQ SN:chr1 LN:247249719 @SQ SN:chr2 LN:242951149 @SQ SN:chr3 LN:199501827 ... That's why this works for me: which <- RangesList(chr1=IRanges(start=1,end=247249719)) Maybe your's might look like: @SQ SN:chromo1 LN:247249719 @SQ SN:chromo2 LN:242951149 @SQ SN:chromo3 LN:199501827 (or something) Then the appropriate call for you would be: which <- RangesList(chromo1=IRanges(start=1,end=247249719)) Does that work for you? -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
