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Reading BAM files

To get started, you'll read mapped reads from a BAM file into R. These files store information about the alignment between read sequences and the reference genome in a compressed binary format. Loading data from BAM files is a common task when analyzing genomic data.

In this exercise, you'll first load all reads from a bam file. This is straightforward but can require a lot of memory, so in the second part, you'll learn how to load only the reads from a region of interest.

This exercise is part of the course

ChIP-seq with Bioconductor in R

View Course

Exercise instructions

  • Load reads from chr20_bam file using the readGAlignments() function.
  • Create a BamViews object for chr20_bam that covers the region 29805000 - 29820000 on chromosome 20.
  • Use readGAlignments() again to load only the reads in that view.
  • Inspect the reads_sub object using str().

Hands-on interactive exercise

Have a go at this exercise by completing this sample code.

# Load reads form chr20_bam file
reads <- ___(chr20_bam)

# Create a `BamViews` object for the range 29805000 - 29820000 on chromosome 20
bam_views <- ___(___, bamRanges=GRanges("chr20", IRanges(start=29805000, end=29820000)))

# Load only the reads in that view
reads_sub <- ___(___)

# Inspect the `reads_sub` object
___(reads_sub)
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