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

mamba create -n anansnake -c bioconda anansnake

Don't forget to activate the conda environment withmamba activate anansnake.

The anansnake github repository contains anexample folder which can be downloaded to try the workflow.Checkit's README for details!

Anansnake works with seq2science in- & output: The RNA- and ATAC-seqsamples.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 theanansnake column.Which conditions from theanansnake column are compared is set in theconfig.yaml file, undercontrasts.

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

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