About BSJs and FSJs

[andre-gabriel-42]

This is more like a concept question, but I would like to know if the BSJs and FSJs are counted per read or per million reads? How does the algorithm count the number of BSJs? Thanks a lot.

[Kevinzjy]

Hi @andre-gabriel-42 ,

• The BSJs and FSJs are raw number of supporting reads in the dataset without normalization.
• CIRIquant uses a pseudo-circular reference to determine the BSJ reads, and the output BSJs is the number of read pairs that aligned to the BSJ regions with more than 10bp anchor length.

[andre-gabriel-42]

Thank you! 👍