01. Introduction
snakeATAC is a snakemake based end-to-end pipeline to analyze ATAC-seq data. The input files required to run the pipeline are Paired-End fastq files. The pipeline include data quality check and normalization. It is included also a step of data reads shifting in order to take into account the Tn5 transposome insertion bias. Indeed, reads should be shifted +4bp and −5bp for positive and negative strand respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase and achieve base-pair resolution of TF footprint and motif-related analyses (Yan F., et al., Genome Biol. 2020).
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