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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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Brie-Count and Brie-Quant Errors #44

Open ri2gu opened 2 years ago

ri2gu commented 2 years ago

Dear Yuanhua,

On the example you gave on https://brie.readthedocs.io/en/latest/quick_start.html under "Pre-Step: Read Counting" for 10x genomics data, I was unable to execute brie-count or brie-quant, as it kept giving the error that the command "brie-count" and "brie-quant" did not exist. Would you happen to know why it appears as un-executable when I run the command, or what I could do to remediate this error?

Thank you!

huangyh09 commented 2 years ago

Hi, sorry for the delayed reply. It looks that brie-count and brie-quant are not findable in your environment.

Are you using it in the same Conda environment that you installed BRIE2? Which version have you installed?

Yuanhua

ri2gu commented 2 years ago

That must've been the problem! Thank you!

liuyu988 commented 2 years ago

Dear Yuanhua,

On the example you gave on https://brie.readthedocs.io/en/latest/quick_start.html under "Pre-Step: Read Counting" for 10x genomics data, I was unable to execute brie-count or brie-quant, as it kept giving the error that fail to load index for "....bam",reverting to slow method\nsamtools idxstats:... . Would you happen to know what I could do to remediate this error?

Thank you!

huangyh09 commented 2 years ago

@liuyu988 Thanks. Can you elaborate on your issue again? Not sure if I get it.

liuyu988 commented 2 years ago

the error is: [E::idx_find_and_load] Could not retrieve index file for 'cellsorted_possorted_genome_bam.bam'

pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools idxstats: fail to load index for "cellsorted_possorted_genome_bam.bam", reverting to slow method\nsamtools idxstats: file is not position sorted\nsamtools idxstats: failed to process "cellsorted_possorted_genome_bam.bam"\n'

liuyu988 commented 2 years ago

@huangyh09 i have done the samtools index for the bam file and the bai file is stored in the same directory, however, i seems not to find a parameter assign the index file.thanks

huangyh09 commented 2 years ago

Hi @liuyu988, it seems a different issue in your case. I wonder whether this is because your bam file is sorted by cell instead of genomic position. Could you double-check? We only tested on possorted (position sorted) as cellranger output and it worked well.

Yuanhua