Required files for RNA velocity (mouse version)

zakiF commented 5 years ago

Hi,

Not sure if this post is considered an issue or leaning more to a question. The RNA velocity tutorial provided links to download materials for human genome, for instance ;

Human cDNA Transcripts
Human introns Transcripts
cDNA Transcripts to Capture
Introns Transcripts to Capture
cDNA/introns Transcripts to Genes map

I was wondering if the required files for mouse version can be provided as well? In addition I am hoping to use the bustools / RNA velocity workflow from SmartSeq2 sequencing fastq files, is the current workflow compatible for SmartSeq protocol?

Best Zaki

lambdamoses commented 5 years ago

Sorry for the confusion. We will post a tutorial on how to generate those files soon, later this week or next week. I don't think the kallisto bus pipeline will work for SmartSeq2. The technology must be UMI based (the u in bus means UMI). Use kallisto bus --list to see the list of technologies supported.

sbooeshaghi commented 5 years ago

The files to reproduce figure 3 in the manuscript (mouse) are located here:

https://github.com/pachterlab/MBGBLHGP_2019/releases/tag/figure_3_files

BUStools / getting_started

Required files for RNA velocity (mouse version) #1