Understanding of parameter --max-junction-splice-size

[sanyalab]

Hello,

This is not an issue. But I wanted to understand if "--max-junction-splice-size" parameter refers to max intron length. Similarly "--min-junction-splice-size" refers to minimum intron length.

Thanks
Abhijit

[ruolin]

You are right. This is the max intron size since some aligners sometimes falsely output splice alignment with junction size too big to be true.

[sanyalab]

Ok. Super. Thank you.