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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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UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte #34

Closed Byronxy closed 4 years ago

Byronxy commented 4 years ago

Hi, I set up the environment as you described. And I tested with the example data and got the error. image

huangyh09 commented 4 years ago

Hi, thanks for the testing. BRIE2 takes a list of sam files in the -S option instead of each sam file.

Please follow the quick start example: https://brie.readthedocs.io/en/latest/quick_start.html or the the new demo file: https://github.com/huangyh09/brie/blob/master/examples/brie2_demo.sh

Also, please upgrade to v2.0.2 from github

pip install -U git+https://github.com/huangyh09/brie

Let us know if it resolves your issue.

Yuanhua

Byronxy commented 4 years ago

Hi, I successfully run the brie_count. However, I got an error when running brie-quant image

huangyh09 commented 4 years ago

Good. It looks you only have three cells, and all genes are filtered out, as by default --minCell=30, namely only genes having >= 30 cells with unique reads are kept. You could set --minCell=0.

Byronxy commented 4 years ago

Thanks a lot! I got the result! image