Pipelines for preprocessing of ATAC/ChIP-seq, RNA-seq and scRNA-seq data.

• the environment.yml contains a Linux conda environment (built on CentOS-7) with all required software

• a Docker image based on that environment is available from the Docker Hub

Run any of the bash scripts without arguments or with -h/--help to see the help section with all available arguments.

Deprecated: Use this Nextflow pipeline instead => https://github.com/ATpoint/rnaseq_preprocess

Deprecated: Use this Nextflow pipeline instead => https://github.com/ATpoint/sc_preprocess

Deprecated: Use this Nextflow pipeline instead => https://github.com/ATpoint/atac_chip_preprocess

Deprecated: Use this https://github.com/ATpoint/bam2bedgraph, still bash-based but a more cleaned-up version that is simpler and includes the averaging script from below plus a Docker image and conda environment YAML file.

Deprecated: See https://github.com/ATpoint/bam2bedgraph.