[BioC] Amplicon and exon level read counts and GC content

Martin Morgan mtmorgan at fhcrc.org
Wed May 30 07:44:51 CEST 2012

On 05/29/2012 10:17 PM, Yu Chuan Tai wrote:
> Hi,
> I have some questions about DNA-Seq and RNA-Seq analyses. In Amplicon
> sequencing, is there any package/function which can extract
> amplicon-level read counts and GC content from an aligned file of BAM
> format? The same question to exon-level read counts and GC content. More
> generally, given a genomic interval, how could I extract the read count
> and GC content for that interval?

The Rsamtools package has scanBam for read input, also 
GenomicRanges::readGappedAlignments and GenomicRanges::summarizeOverlaps 
for higher-level read counting. The requirement is generally a 
'GRanges', which can be queried from TxDb packages (e.g., 
TxDb.Hsapiens.UCSC.hg19.knownGene) or from gff (via rtracklayer) or many 
other sources. There are vignettes in GenomicRanges, GenomicFeatures, 
rtracklayer, and Rsamtools packages; see



> Thanks for any input!
> Best,
> Yu Chuan
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