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Old 02-27-2017, 03:28 PM   #1
gstone
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Default BBRepair quality score changes

After running BBRepair the log file states: "Changed from ASCII-33 to ASCII-64 on input quality 97 for base C while prescanning." It does this for base scores 66, 95, and 98. I would like to run the files through quality trimming, but am now unsure how the quality scores are encoded (sanger, illumina, etc). Prior to BBRepair, some files had sanger scores, and other had illumina. Any help would be greatly appreciated.
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Old 02-27-2017, 03:44 PM   #2
Brian Bushnell
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If the encoding was detected correctly, or if you add the flag "changequality=f", the output will retain the same encoding as the input. It's always best to tell it what the encoding is, though, because it is not possible to detect the quality score encoding with 100% accuracy. You can specify encoding with these flags:

qin=64 qout=33


That will force the input to be treated as ASCII-64 (old Illumina) and the output will be ASCII-33 (Sanger). It's normally easiest to work with data when all sets have the same encoding...
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Old 02-27-2017, 07:01 PM   #3
gstone
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Thank you for your quick response. Even though the log file says the quality encoding changes, when I check the file's quality encoding with testformat.sh in bbmap (from your comment here https://www.biostars.org/p/63225/), the output states that the file is in its original encoding. I was hoping you could clarify whether repair.sh permanently or temporarily changes quality encoding.

Thank you!!

Last edited by gstone; 02-27-2017 at 07:13 PM.
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Old 02-28-2017, 07:33 AM   #4
Brian Bushnell
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Sorry, I guess the message is unclear. When it says this:

"Changed from ASCII-33 to ASCII-64 on input quality 97 for base C while prescanning."

That means it started with the assumption that your data is in ASCII-33, but examined the file, and decided the input was ASCII-64. So, it processed the file assuming the data was ASCII-64. In that case, it does not change the data at all - what changes is the assumption about how to interpret the data. In other words, your data is unchanged.
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Old 02-28-2017, 01:54 PM   #5
gstone
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Great, thank you so much for the clarification!
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Old 02-28-2017, 02:27 PM   #6
GenoMax
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If your data is in phred+64 format (only possible if it is pretty old) then remember to use qin=64 option with other bbtools.
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