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.