gene.gene.txt no symbols

BUStools / bustools

Tools for working with BUS files

https://bustools.github.io/

BSD 2-Clause "Simplified" License

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gene.gene.txt no symbols #48

Closed BarryDigby closed 3 years ago

BarryDigby commented 4 years ago

I have followed the "getting started" tutorial and generated the barcodes, genes and mtx files. The gene.genes.txt file does not have the corresponding gene symbols.

I read elsewhere that cellranger outputs a genes file with 2 columns, ID + Symbol

I have tested a different dataset from 10X genomics and get the same result.. is this expected behaviour?

This is being addressed on biostars

I am sorry, I did not realise your team monitored posts there. Can you delete this message please?

soohyuna commented 4 years ago

I ran into the same problem!! Has this issue been solved?

BarryDigby commented 4 years ago

@soohyuna I wrote about how to fix this using python scripts developed by the Kallisto team.

https://github.com/BarryDigby/scRNA-Seq/blob/master/an_unbridled_rage.md

p.s You might want to use kb_python wrapper tool instead of kallisto bustools. At the time I came across this error, the Kallisto team were rolling out kb_python so I didn't know any better!

soohyuna commented 4 years ago

@BarryDigby Thank you for the link!

sbooeshaghi commented 3 years ago

@BarryDigby thanks for the tutorial showing how to augment gene ids with their names.