Commit 3d62098c authored by Blaise Li's avatar Blaise Li
Browse files

Switched to new small RNA classification.

This is not yet fully tested, and may have effects on other pipelines.
parent 2807a83a
......@@ -275,8 +275,11 @@ def aligner2min_mapq(aligner, wildcards):
What minimal MAPQ value should a read have to be considered uniquely mapped?
See <>.
mapped_type = wildcards.mapped_type
if mapped_type.startswith("unique_"):
mapping_type = wildcards.mapping_type
except AttributeError:
mapping_type = wildcards.mapped_type
if mapping_type.startswith("unique_"):
if aligner == "hisat2":
return "-Q 60"
elif aligner == "bowtie2":
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