Hello Yang @goldenflaw !
I hope I am not bothering you too much.
In leafcutter_cluster_regtools.py -> refine_cluster(), the junction filtering if-statement is: if (count / float(totN) >= cutoff and count >= readcutoff), where count is the junction count, and not the total cluster count.
This is inconsistent with the --help, which states that minreads is the minimum number of reads in a cluster.
Indeed, in the *_refined file, all junctions have reads >= minreads.
A related question: is it better to set per-junction read cutoff, or to set per-cluster read cutoff?
Sincerely,
Boxiang
Hello Yang @goldenflaw !
I hope I am not bothering you too much.
In
leafcutter_cluster_regtools.py->refine_cluster(), the junction filtering if-statement is:if (count / float(totN) >= cutoff and count >= readcutoff), where count is the junction count, and not the total cluster count.This is inconsistent with the
--help, which states thatminreadsis the minimum number of reads in a cluster.Indeed, in the
*_refinedfile, all junctions have reads >=minreads.A related question: is it better to set per-junction read cutoff, or to set per-cluster read cutoff?
Sincerely,
Boxiang