Hi ALL, Given BAM file, I like to get output something like below. Any ideas? Chr Position DepthOfCoverage BaseCounts chr1 14112 14 A:0 C:0 G:0 T:14 N:0 chr1 14113 13 A:0 C:13 G:0 T:0 N:0 chr1 14114 11 A:0 C:0 G:0 T:11 N:0 chr1 14115 11 A:10 C:0 G:0 T:1 N:0 Many thanks in advance. Best Regards Chandu -- output of sessionInfo(): R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.

Hi Chandu, The 'applyPileups' in the 'Rsamtools' packages will help you here: "An array of dimensions nucleotide x file x position. The ?nucleotide? dimension is length 5, corresponding to ?A?, ?C?, ?G?, ?T?, and ?N? respectively." (Taken from the 'Rsamtools' manual) The coverage you can then get with a function like 'rowSums'. Best wishes Julian On 08/29/2013 09:58 AM, Chandu [guest] wrote: > > Hi ALL, > > Given BAM file, I like to get output something like below. Any ideas? > > > Chr Position DepthOfCoverage BaseCounts > chr1 14112 14 A:0 C:0 G:0 T:14 N:0 > chr1 14113 13 A:0 C:13 G:0 T:0 N:0 > chr1 14114 11 A:0 C:0 G:0 T:11 N:0 > chr1 14115 11 A:10 C:0 G:0 T:1 N:0 > > Many thanks in advance. > > Best Regards > Chandu > > -- output of sessionInfo(): > > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 >