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bioinfo-biols / CIRI-long

Circular RNA Identification for Nanopore Sequencing
https://ciri-cookbook.readthedocs.io
MIT License
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how could i get the isoforms' counts? #11

Open koosle opened 2 years ago

koosle commented 2 years ago

Dear author, As the title, is there any function in CIRI-long to catch isoforms' counts ? Or how could I get isoforms' counts instead of circRNA-genes' counts ?

Thanks a lot.

Kevinzjy commented 2 years ago

hi @koosle , the 640474e1275dec0d5b6ec556d16e6b118499de60 commit will generate the matrix of isoform usage, which is similar to the percentage of spliced in (PSI) values in alternative splicing analysis.

In CIRI-long, the circRNA bsj count includes full-length reads, partial reads, and ambiguous mapped reads. So it's hard to give the exact number of isoform bsj counts. I would suggest you do differential analysis on the circRNA level, then test the change of isoform usage separately.