Vireo (Variational inference for reconstructing ensemble origins), a Bayesian method to demultiplex pooled scRNA-seq data without genotype reference. Vireo is primarily designed demultiplexing cells into donors by modelling of expressed alleles. It supports a variety of settings of donor genotype (from entirely missing, to partially missing, to fully observed). As a general cell clustering methods by allelic ratio (equivalent to genotyping), Vireo is applicable for more settings besides donor demultiplexing, including reconstruction of somatic clones, see vireoSNP_clones.ipynb for example on mitochondral mutations.
https://vireosnp.readthedocs.io/en/latest/
- Module Name: vireosnp (see the modules page for more information)
- Example files are under /usr/local/apps/vireosnp/example
Allocate an interactive session and run the interactive job there.
[biowulf]$ sinteractive --mem=5g
salloc.exe: Granted job allocation 789523
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0135 are ready for job
[cn0135]$ mkdir /data/$USER/vireosnp
[cn0135]$ module load vireosnp
[cn0135]$ cp -r /usr/local/apps/vireosnp/{examples,data} /data/$USER/vireosnp
[cn0135]$ bash /data/$USER/vireosnp/examples/demo.sh
[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.
[biowulf]$
1. Create a script file (myscript) similar to the one below
#! /bin/bash # myscript set -e module load vireosnp || exit 1 cd /data/$USER/test/ vireo -c $CELL_DIR -N 4 -o $OUT_DIR --randSeed 2
2. Submit the script on biowulf:
[biowulf]$ sbatch --mem=5g myscript
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/$USER/cmdfile).
cd /data/$USER/dir1; vireo -c $CELL_DIR -N 4 -o $OUT_DIR --randSeed 2 ... cd /data/$USER/dir2; vireo -c $CELL_DIR -N 4 -o $OUT_DIR --randSeed 2 ... cd /data/$USER/dir3; vireo -c $CELL_DIR -N 4 -o $OUT_DIR --randSeed 2 ... ... cd /data/$USER/dir20; vireo -c $CELL_DIR -N 4 -o $OUT_DIR --randSeed 2 ...
submit the swarm job:
$ swarm -f cmdfile --module vireosnp -g 5
For more information regarding running swarm, see swarm.html