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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 spling types filter (A5SS, A3SS, MXE, RI) #11

Open chenjiwei124128 opened 6 years ago

chenjiwei124128 commented 6 years ago

Hi, I did not see any examples analyzing other splicing types (A5SS, A3SS, MXE, RI) using BRIE. I used brie-event-filter to deal with gff3 of other splicing types, but I can not get gold.gtf or gold.gff3.

huangyh09 commented 6 years ago

Hi Jiwei,

At current version, BRIE only quantify exon skipping events, as this type of splicing events can be predicted well from the sequence features. Others, e.g., A3SS, are more difficult to be predicted, so not included yet.

If you want to use the sequence aiding free quantification for other splicing events, you could try my another splicing quantification method, DICEseq: https://github.com/huangyh09/diceseq. It can deal with all types of splicing events (designed for bulk) but don't use sequence features.

Best, Yuanhua

chenjiwei124128 commented 6 years ago

Thanks for your reply!