Anansnake

Link seq2science output to ANANSE with 2 sample tables and one config file.

Installation

mamba create -n anansnake -c bioconda anansnake

Don’t forget to activate the conda environment with mamba activate anansnake.

Running anansnake on the example data

The anansnake github repository contains an example folder which can be downloaded to try the workflow. Check it’s README for details!

Running anansnake

Anansnake works with seq2science in- & output: The RNA- and ATAC-seq samples.tsv files are the same you’ve used for seq2science, with one addition (see below). The counts tables are output files without any changes.

The RNA- and ATAC-seq samples are combined via a shared column in the samples.tsv files. In the example data, this is the anansnake column. Which conditions from the anansnake column are compared is set in the config.yaml file, under contrasts.

For files and settings & command line examples you can check out the example folder.

Troubleshooting

ANANSE can take tonnes of memory. If your machine freezes, reduce the number of threads or mem_mb.