Hello,
I am trying to analyze 16s Illumina V3/V4 Miseq Data. They are already demultiplex the primers are already removed.
But I double check to see if the overhang adapters are also removed and I can still find them in my fastq-File (in about 5-20 sequences per fastq-File). (I checked only a few of my fastq files.)
So far, I only found the forward overhang adapter - but I didn't find them right at the beginning, sometimes some bp into the sequence.
These are the adapters:
Forward overhang: 5ā TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGā[locusspecific
sequence]
Reverse overhang: 5ā GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGā[locusspecific
sequence]
My question is: Will the cutadadpt command also remove these if the adapter is located somewhere in the middle of the sequence?
Thanks in advance!