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huangyh09 / brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells
https://brie.readthedocs.io
Apache License 2.0
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the output of brie-count don't contain the .h5ad file #47

Open liuyu988 opened 2 years ago

liuyu988 commented 2 years ago

Hi Yuanhua,

my code is as follows:

brie-count -a genes.gff3 -S cell.bam -b barcodes.tsv.gz -o test2/ -p 15 -t any

this process ran for 15 hours, however, the result files don't contain the improtant .h5ad file.

Is anything i miss? thanks

huangyh09 commented 2 years ago

How many genes and cells are you using? It's not fast but generally OK (~1h) for thousands of cells/genes.

Yuanhua

huangyh09 commented 2 years ago

In v2.2.1, we now support output h5ad file if all genes only have two isoforms, no matter what splicing event types. you may consider re-run it with the new version.

Y

liuyu988 commented 2 years ago

In v2.2.1, we now support output h5ad file if all genes only have two isoforms, no matter what splicing event types. you may consider re-run it with the new version.

Y

Thank you for your reply! I have run this code for ~15 hours and the version i used is v2.2.0, I will try to use v2.2.1