README.md

MACSIMA pipeline for hpc usage

Bashscripts to stage, apply illumination correction and run mcmicro on MACSima data

This is work on progress, currently only the staging script is available (staging.sh). The steps to use this are:

1. download the container of macsima2mc with the following command:

singularity pull docker://ghcr.io/schapirolabor/multiplex_macsima:v1.0.0

2. Create a tab separated sample array file (e.g. acquisitions.tsv) with two columns: ArrayTaskID and Sample. The former is an integer number that represents the TaskID, the latter is the absolute path of the folder that contains the cycles of the acquisition.

3. Create a directory for the outputs of the staging tool, e.g. output_dir.

4. Open the staging.sh file and specify the following inputs: -SBATCH --array=1 : range of samples to take from the ArrayTaskID, in this example we only have ID 1, if n samples then,

   SBATCH --array=1-n
   

   -acquisitions : path to the sample array file

   acquisitions=/myarrays/acquisitions_array.tsv
   

   -staging_container=absolute path to the macsima2mc container, downloaded in step 1.

   staging_container=/mycontainers/multiplex_macsima_v1.0.0.sif
   

   -output_dir=absolute path to the created output_dir folder

   output_dir=/home/output_dir
   

   

5. Save the changes to the staging.sh file and run it:

sbatch staging.sh

6. Once the staging script is over the restructured MACSima data sets will be found in the output_dir. The data of a cycle will be written into two ome.tiff files, one file containes the marker signal (src- S) and the other one the backround signal (src- B).