Question: Rsamtool or Rbamtools function to view the number of reads between a range
0
gravatar for startup_biostar
4.1 years ago by
startup_biostar10 wrote:

what is Equivalent R function for the command line below?

samtools view yourBAMfile.bam chr1:567876-568100 | wc -l

How should I approach.

I got a GRanges object with seqnames, start and end. I would like to count the number of reads between each range in the GRange object in a BAM file in R

rsamtools rna-seq rbamtools R • 1.1k views
ADD COMMENTlink modified 4.1 years ago by Devon Ryan95k • written 4.1 years ago by startup_biostar10
2
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

rbamtools directly provides a count function (bamCount), so just go with that.

ADD COMMENTlink written 4.1 years ago by Devon Ryan95k
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