Hi,
Is there an official way to run BWA0.6.1 for fastq files with the Illumina 1.8+ encoding for quality?
From my reading there are 2 possibilities:
1. Convert Illumina 1.8+ to Sanger in all fastq files, then run alignment (no -I parameter).
2. Run BWA (no -I parameter) and hope qualities are interpreted correctly.
Which is officially advised?
Thank you
Is there an official way to run BWA0.6.1 for fastq files with the Illumina 1.8+ encoding for quality?
From my reading there are 2 possibilities:
1. Convert Illumina 1.8+ to Sanger in all fastq files, then run alignment (no -I parameter).
2. Run BWA (no -I parameter) and hope qualities are interpreted correctly.
Which is officially advised?
Thank you
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