Computing coverage
Now it is time for you to extend reads to the average fragment length to obtain a better coverage estimate. Extending the reads allows you to combine reads from both ends of a fragment into a single coverage peak, which helps to distinguish peaks from the background noise.
The BAM file for sample GSM1598218 that you will be using for this exercise has already been loaded for you. The average fragment length for this sample is 183 bp. The reads are available as a GRanges object called reads_gr.
It may take a moment to load all required data and R packages for this exercise. Please be patient.
This exercise is part of the course
ChIP-seq with Bioconductor in R
Exercise instructions
- Extend reads to the average fragment length.
- Compute the fragment coverage.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Extend reads to the average fragment length of 183 bp
reads_ext <- ___(reads_gr, width=___)
# Compute coverage
cover <- ___(___)