Hello, I’m having an issue with summary.qual, I sequenced my DNA with Illumina and got a lot of very high quality reads, and when I use summary.qual I get this error:
[ERROR]: 36-illcus515F__A00769_42_HV3CFDRXX_1_2104_11695_30044 has a quality scores of 42, expecting values to be less than 40.
Is there any way to change it so it expects higher quality scores than <40?
Thank you for bringing this to my attention. I will change error message to be a warning that does not cause the command to fail. This change will be available in our next release.
@westcott: based on the table in this - https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote_understanding_quality_scores.pdf - I think we should convert scores over 40 as 40 for processes internal to mothur
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