In todays session we will work with some of the ATAC-seq data of T-regulatory cells from Christina Leslie’s lab.
FQ files can be found can be found here for read1 and here for read2.
We will also work with the aligned data as a BAM file which can be found here.
Optional Align the reads in hg38 genome and create sorted, indexed BAM file.
Using the BAM file retrieved from ENCODE, plot the fragment length distribution for reads chromosome 10 using ggplot2.
6 Create a bigwig for the nucleosome free (< 100bp), mono-nucleosome (180bp-247bp) and di-nucleosome (315-437) fractions and visualise in IGV.