search

velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
160 stars 83 forks source link

gene name issue #357

Closed YichaoOU closed 1 year ago

YichaoOU commented 1 year ago

Hello,

I'm having a name inconsistency issue. Some gene names in the loom file produced by velocyto are different than gene names in seruat.

The loom files are generated by: velocyto run10x --samtools-threads $ncore -m $repeats $COL1 $transcriptome. Then ldata = scv.read(sample_dir, cache=False)

Example 1: the gene name is Aldoa, but velocyto add -1, which becomes Aldoa-1.

Example 2: the gene name is Ighd1-1, but becomes Ighd1.

What is wrong?

Thanks, Yichao

YichaoOU commented 1 year ago

I seem to find the reason. These genes have two Ensembl IDs with the same gene name, seurat renamed the second duplicate as .1 and velocity renamed the second one as -1