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.