Commit 58a71439 authored by Blaise Li's avatar Blaise Li
Browse files

Factorized code (MAPQ filtering, RPK, rTRPM).

parent fd4e0679
......@@ -268,6 +268,25 @@ def make_seeding_function(seeding_string):
return seeding_function
def aligner2min_mapq(aligner, wildcards):
Option to filter on MAPQ value in featureCounts.
What minimal MAPQ value should a read have to be considered uniquely mapped?
See <>.
mapped_type = wildcards.mapped_type
if mapped_type.startswith("unique_"):
if aligner == "hisat2":
return "-Q 60"
elif aligner == "bowtie2":
return "-Q 23"
raise NotImplementedError(f"{aligner} not handled (yet?)")
return ""
## Not sure this is a good idea...
# def masked_gmean(a, axis=0, dtype=None):
# """Modified from"""
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment