Bioconductor Exercises Part 1

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Exercises

1. Import human hg19 gene coordiantes from “./data/hg19Genes.txt” and create a GRanges of Transcription start sites (1 bp range).
   • Tip: How to identify TSS for genes in forward/reverse strand?
2. Create a GRanges object of human promoters with TSS ± 2000bp.
   • Tip: Read the documentation for promoters function.
3. Import ELF1 binding sites in K562 cell from Encode (./data/ELF1_K562.bed) and create GRanges object.
   • Tips: Import the ELF1 binding sites using import.bed() function from rtracklayer package
   • Find ELF1 binding sites overlap with promoters (TSS ± 1kb) using findOverlaps and subsetByOverlaps (Remember BED format uses 0-based coordinates)