Tuesday 28 August 2018

STAR Aligner In Retion to Phred Quality Encoding

Cited from Phred64 encoding consideration in STAR

"""
STAR does not need to phred quality encoding, at the moment it does not actually use quality scores for mapping. It will simply copy the quality strings into SAM output. If you want to convert the quality scores output is SAM for some reason, you can use --outQSconversionAdd <positive or negative number>.
"""

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