9.2 Run SJARACNe

By default, the generateSJARACNeInput() function also generates a runSJARACNe.sh file in the folder of each group. This file much be modified before you can run it:

  • removed unneeded lines: There are usually 4 lines in this file: the lines starting with “sjaracne lsf” are the command lines to run on IBM LSF cluster, while the lines starting with “sjaracne local” are the command lines runing on a single machine (Linux/OSX). Please select the lines based on your situation and remove the others.
  • -n: number of bootstrap networks to generate. Default: 100.
  • -pc: p value threshold to select edges in building consensus network. Default: e-2 for single-cell data, e-3 for meta-cell data, and e-5 for bulk sample data. Please use “sjaracne lsf -h” or “sjaracne local -h” to check more details of arguments available in SJARACNe.

There is another file, config_cwlexec.json, available in the folder. It contains the information (e.g. memory request for each step of SJARACNe run) used for LSF job submission. This file is only needed for LSF runs and the default values works well in most cases. If you are running SJARACNe on a big dataset, you may need to request more memory from it.

In this case, we use LSF to run the SJARACNe:

## let's use B cell as an example
# for TF
sjaracne lsf -e /work-path/PBMC14k/SJARACNe/B/B.8572_1902.exp.txt -g /work-path/PBMC14k/SJARACNe/B/TF/B.835_1902.tf.txt -o /work-path/PBMC14k/SJARACNe/B/TF/bt100_pc001 -n 100 -pc 0.01 -j /work-path/PBMC14k/SJARACNe/B/config_cwlexec.json

# for SIG
sjaracne lsf -e /work-path/PBMC14k/SJARACNe/B/B.8572_1902.exp.txt -g /work-path/PBMC14k/SJARACNe/B/SIG/B.4148_1902.sig.txt -o /work-path/PBMC14k/SJARACNe/B/SIG/bt100_pc001 -n 100 -pc 0.01 -j /work-path/PBMC14k/SJARACNe/B/config_cwlexec.json

We created a folder named “bt100_pc001” in both TF and SIG folders of each group, to save the networks generated under 100 bootstraps (-n 100) and 0.01 consensus p value (-pc 0.01).

To run SJARACNe on a local machine:

## let's use B cell as an example
# for TF
sjaracne local -e /work-path/PBMC14k/SJARACNe/B/B.8572_1902.exp.txt -g /work-path/PBMC14k/SJARACNe/B/TF/B.835_1902.tf.txt -o /work-path/PBMC14k/SJARACNe/B/TF/bt100_pc001 -n 100 -pc 0.01

# for SIG
sjaracne local -e /work-path/PBMC14k/SJARACNe/B/B.8572_1902.exp.txt -g /work-path/PBMC14k/SJARACNe/B/SIG/B.4148_1902.sig.txt -o /work-path/PBMC14k/SJARACNe/B/SIG/bt100_pc001 -n 100 -pc 0.01