Other AS types counting, no output about brie HOT 6 OPEN

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

LiuYu

from brie.

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

LiuYu

Not yet.

from brie.

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

from brie.

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

from brie.

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

from brie.

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

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