Other spling types filter (A5SS, A3SS, MXE, RI)

[chenjiwei124128]

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]

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]

Thanks for your reply!