velocyto

Version:: 0.17.17
Category:: bio
Cluster:: Loki

Author / Distributor

Description

Package for the analysis of expression dynamics in single cell RNA seq data

Documentation

Usage: velocyto [OPTIONS] COMMAND [ARGS]...

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  run            Runs the velocity analysis outputting a loom file
  run10x         Runs the velocity analysis for a Chromium Sample
  run-dropest    Runs the velocity analysis on DropEst preprocessed data
  run-smartseq2  Runs the velocity analysis on SmartSeq2 data (independent bam file per cell)
  tools          helper tools for velocyto

Examples/Usage

Load the velocyto module:
```
$ module load velocyto
```
Check the loaded modules:
```
$ module list
```
List available modules:
```
$ module avail velocyto
```
Unload the velocyto module:
```
$ module unload velocyto
```

Run velocyto for standard BAM files:

$ velocyto run -b barcodes.tsv -o output/ sample.bam annotation.gtf

Run velocyto for 10x Genomics data:

$ velocyto run10x -o output/ /path/to/10x_folder annotation.gtf

Convert velocyto output format:

$ velocyto convert -o converted_output.h5ad output.loom

Merge multiple loom files:

$ velocyto merge merged_output.loom sample1.loom sample2.loom

Installation

Source code is obtained from Velocyto