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trimmomatic V0.39, keepBothReads: flag or boolean? #16

Closed TeiturAK closed 2 years ago

TeiturAK commented 2 years ago

Hi,

following your example commands in the Quick start guide at https://github.com/usadellab/Trimmomatic and http://www.usadellab.org/cms/?page=trimmomatic it seems that keepBothReads is a flag that is passed to trimmomatic V0.39 and not a boolean value as in the manual for earlier versions, http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf.

Running trimmomatic V0.39 with ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads does however not produce the same results as ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:TRUE. With TRUE there are more surviving read pairs while setting keepBothReads (or a random word) retains fewer.

To me it looks like TRUE is the correct way of setting this parameter but in your posted examples this looks like a flag. Please advice.

TonyBolger commented 2 years ago

Well spotted, and you are correct - keepBothReads is the name of the flag, and its should be a boolean. I have corrected the README accordingly.

KuechlerO commented 2 years ago

@TonyBolger Kindly also consider the documentation on this page, which still displays it in the example as a flag.