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Reading BED files

In this exercise, you will load peak calls from a BED file and use the information about peak locations to extract reads that overlap with the peaks from a BAM file.

This exercise is part of the course

ChIP-seq with Bioconductor in R

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Exercise instructions

  • Use the import.bed function to load peak calls from chr20_peaks.
  • Use these peak calls to create a BamViews object for chr20_bam.
  • Load the reads overlapping with the peak calls.

Hands-on interactive exercise

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

# Load peak calls from chr20_peaks
peaks <- ___(chr20_peaks)

# Create a BamViews object
bam_views <- ___(___, bamRanges=peaks)

# Load the reads
reads <- ___(___)
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