October 2023 #4
Description
ATAC sequencing data analysis
Alignment of raw reads using Bowtie2
Filtering out low quality reads, duplicates, and reads that map to mitochondrial DNA
Cell barcode and UMI processing using information from 10x genomics library
Peak Calling using MACS2, HOMER or GEM
Annotation identified peaks
Differential accessibility analysis: compare peaks between saline and fentanyl
Pathway analysis (not sure how to do this...)
Visualization using ATACSeqQC or deepTools