[BioC] Coverage of reads per base position from BAM files

[Rithun Mukherjee [guest]]

I am trying to obtain per reference base position coverage for a BAM file. The BAM file has been generated by Samtools and contains alignment info for 10 million reads to a 7kb reference plasmid genome. What is the best way to go about this? I have explored the "readBamGappedAlignments" and "readAligned" functions but I am not sure of the way forward from there.

Also should I be using a BAM file or the sorted BAM file with its corresponding index file? I am currently using the later.

Thanks much.


 -- output of sessionInfo(): 

R version 2.14.2 (2012-02-29)
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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 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_1.12.4    latticeExtra_0.6-19 RColorBrewer_1.0-5 
[4] lattice_0.20-6      Rsamtools_1.6.3     Biostrings_2.22.0  
[7] GenomicRanges_1.6.7 IRanges_1.12.6     

loaded via a namespace (and not attached):
 [1] Biobase_2.14.0     bitops_1.0-4.1     BSgenome_1.22.0    grid_2.14.2       
 [5] hwriter_1.3        RCurl_1.91-1       rtracklayer_1.14.4 tools_2.14.2      
 [9] XML_3.9-4          zlibbioc_1.0.1    


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