This is repository of my personal notes from 3 day module of Epigenomics from Bioinformatics Institute for students of Systems Biology and Bioinformatics.
By Oleg Shpynov([email protected]) and Roman Chernyatchik([email protected]).
Due to fastq's being large please download them from here.
Conventional ChIP-Seq ● H3K27ac: GSM1102782 https://www.encodeproject.org/experiments/ENCSR012PII/ ● H3K4me1: GSM1102793 https://www.encodeproject.org/experiments/ENCSR400VWA/ ● H3K4me3: GSM1102797 https://www.encodeproject.org/experiments/ENCSR796FCS/ ● H3K36me3: GSM1102788 https://www.encodeproject.org/experiments/ENCSR244XWL ● H3K27me3: GSM1102785 https://www.encodeproject.org/experiments/ENCSR080XUB/
Download GSM3074495 FASTQ Files
Align them to hg19 reference genome (which you also need to download)
Then extract all the reads aligned to Chromosome 15 and you'll be ready to go.
Alternatively, here is a docker script with stand-alone scripts.
https://github.com/ctlab/sysbio-training/tree/master/masters-2019/epigenetics