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
Exercise instructions
- Use the
import.bedfunction to load peak calls from chr20_peaks. - Use these peak calls to create a
BamViewsobject 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 <- ___(___)