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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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Other AS types counting, no output #45

Open zhaoshuoxp opened 2 years ago

zhaoshuoxp commented 2 years ago

Hi Yuanhua,

I am using v2.2 to count other types of AS, A3SS for example:

brie-count -a ~/genome/mm10/mouseAS/A3SS.gff3 -o . -S bamfile.list -p 8 -t Any

Even with -t Any option, this command still gives error message and stuck like forever:

[BRIE2] example head cells: [['/..../116434_42_3.bam' '116434_42_3'] ['/..../116434_61_39.bam' '116434_61_39'] ['/..../116434_8_46.bam' '116434_8_46']] ... [BRIE2] loading gene annotations ... Done. [BRIE2] counting reads for 6104 genes in 3140 sam files with 8 cores... This is not exon-skipping event! None This is not exon-skipping event! None This is not exon-skipping event! None

Did I miss anything or put something wrong?

Many thanks!

Quanyi

liuyu988 commented 2 years ago

Hi Quanyi， Have you sovled this problem?i seem to meet the problem similar to yours. thanks!

LiuYu

zhaoshuoxp commented 2 years ago

Hi Quanyi， Have you sovled this problem?i seem to meet the problem similar to yours. thanks!

LiuYu

Not yet.

huangyh09 commented 2 years ago

Thanks both for trying out the new feature on other splicing types. Sorry it's actually a minor bug in the code, as we only tested the other splicing events in droplet data.

Now, it has been fixed to support smart-seq in the new release v2.2.1. Please upgrade your package, e.g., by pip install -U brie and try your command line again.

Yuanhua

liuyu988 commented 2 years ago

Thanks both for trying out the new feature on other splicing types. Sorry it's actually a minor bug in the code, as we only tested the other splicing events in droplet data.

Now, it has been fixed to support smart-seq in the new release v2.2.1. Please upgrade your package, e.g., by pip install -U brie and try your command line again.

Yuanhua

Thank you for your reply! Yu

TuoCai2000 commented 2 years ago

Hi Quanyi, I notice that you use the command brie-count with annotation '/genome/mm10/mouseAS/A3SS.gff3' , can you tell me how to generate it? like intron retension and A3SS.etc Thank you!

Tuo

zhaoshuoxp commented 2 years ago

Hi Quanyi, I notice that you use the command brie-count with annotation '/genome/mm10/mouseAS/A3SS.gff3' , can you tell me how to generate it? like intron retension and A3SS.etc Thank you!

Tuo

HI Tuo, I simply use the briekit (https://github.com/huangyh09/briekit/wiki) to generate them from GENCODE GTF file. Please note that the filtering function of it does not work on my end so I just use the unfiltered GFF to proceed. Quanyi