how could i get the isoforms' counts?

[koosle]

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]

hi @koosle , the 640474e 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.