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

[Wei Shi]

Dear Yu Chuan,

You may consider using the featureCounts function in Rsubread package to count the number of reads for the features you are interested in. The built-in RefSeq annotation will allow you to get exon-level read counts. But to get amplicon-level read counts or read counts in a specific genomic interval, you'll have to provide an annotation file to this function to let it count reads for you. 

This function accepts SAM files as input, but I guess you can convert your BAM files to SAM files.  For you information about this function, see ?featureCounts.

Hope this helps.

Cheers,
Wei

On May 30, 2012, at 3:17 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?
> 
> Thanks for any input!
> 
> Best,
> Yu Chuan
> 
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