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

Yu Chuan Tai yuchuan at stat.berkeley.edu
Wed May 30 07:17:29 CEST 2012


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?

Thanks for any input!

Yu Chuan

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