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Commit 3d62098c authored by Blaise Li's avatar Blaise Li
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Switched to new small RNA classification.

This is not yet fully tested, and may have effects on other pipelines.
parent 2807a83a
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...@@ -275,8 +275,11 @@ def aligner2min_mapq(aligner, wildcards): ...@@ -275,8 +275,11 @@ def aligner2min_mapq(aligner, wildcards):
What minimal MAPQ value should a read have to be considered uniquely mapped? What minimal MAPQ value should a read have to be considered uniquely mapped?
See <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>. See <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>.
""" """
mapped_type = wildcards.mapped_type try:
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": if aligner == "hisat2":
return "-Q 60" return "-Q 60"
elif aligner == "bowtie2": elif aligner == "bowtie2":
......
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