Output Data

Solosis CLI generates a number different types of of outputs.

The commands listed below generate outputs in a common place:

• cellranger-count

• cellranger-arc

• starsolo

• iget-fastqs

• iget-cellranger

• cellbender

The outputs for these commands will be found here:

/lustre/scratch126/cellgen/team298/data/samples/

The output file should reflect the tool or command that was executed by solosis, like so:

Tree Diagram of some expected output files on Farm

/lustre/scratch126/cellgen/team298/data/samples/
│       └── cellranger-arc/
|       ├── SAMPLE_ID/
│           ├── cellranger/
│           ├── fastq/
│           ├── starsolo/
│           ├── cellbender/
|           └── ...

Cell Ranger ARC

Cell Ranger ARC outputs will be found here:

/lustre/scratch126/cellgen/team298/data/cellranger-arc/

Tree Diagram of Cell Ranger ARC outputs on Farm

/lustre/scratch126/cellgen/team298/data/cellranger-arc/
│       └── SAMPLE_ID/
│           ├── outs/

Logs

STDOUT and STDERR for commands executed will be found here:

$HOME/logs