Skip to content

Cluster submission of velocyto alignment for RNA velocity analysis.

Notifications You must be signed in to change notification settings

xuesoso/bag_of_velocyto

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

11 Commits
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Logo

Bag of Velocyto

Cluster (Slurm) submission of velocyto alignment for RNA velocity analysis.

Inspired by iosonofabio/Bag of Stars

Work in progress

  • Add usage case

Prerequisites

Convert GFF3 to GTF

Velocyto requires annotation file in the GTF format. I include a custom python script(scripts/convert_gff3_velocyto.py) to convert GFF3 annotation to GTF format suited for Velocyto input. It is recommended that you obtain the GTF annotation whenever possible. My conversion script only converts Exon features to GTF format as they are the only things that Velocyto cares about. Features labeled as repeats will be separately parsed as a repeat_mask file.

About

Cluster submission of velocyto alignment for RNA velocity analysis.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published