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.
Diese Übung ist Teil des Kurses
ChIP-seq with Bioconductor in R
Anleitung zur Übung
- Extend reads to the average fragment length.
- Compute the fragment coverage.
Interaktive Übung
Vervollständige den Beispielcode, um diese Übung erfolgreich abzuschließen.
# Extend reads to the average fragment length of 183 bp
reads_ext <- ___(reads_gr, width=___)
# Compute coverage
cover <- ___(___)