Exercises
- Download the following BAM (aligned to hg19) and index files (.bai)
(ENCODE data - ChIP-Seq of CTCF in Ag04449 human fibroblast cells).
- Use
readGAlignments
to read the bam. Construct an
ScanBamParam
object that accepts only aligned reads,
passing quality control and not duplicates.
- Compute genome wide coverage using
coverage
function
- Export coverage as bigWig using
export.bw()
from
rtracklayer package and visualise it using IGV (https://software.broadinstitute.org/software/igv/download)
- Compute number of reads overlapping with hg19 promoters (TSS ± 1kb)
and export the results as csv file. [hint: use “./data/hg19Genes.txt” to
create the hg19 promoters]