Code for analyzing sequencing data used in the Wenger et al. 2023 study.
Pre-processing, mapping and QC of ChIP/SCAR datasets was performed with the ENCODE's official ChIP-seq pipeline:
https://github.com/ENCODE-DCC/chip-seq-pipeline2
Computation of SCAR-seq Partition files was performed with a modified version of https://github.com/anderssonlab/Replication_SCARseq/blob/master/SCARseq_commands.sh which includes bias correction from stranded inputs and support for paired-end data. See SCAR_processing.sh for usage.
Steps for processing of external datasets can be found in Process_external.R