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ILLUMINACLIP trimming occurs from 5' or 3' for ? #3

Closed marwa38 closed 3 years ago

marwa38 commented 3 years ago

Hi

Could you please let me know from where the trimming happens (5 or 3' end) so that I could set my adpator sequence file correctly?

I am asking about palindrome mode.

Thanks Marwa

TonyBolger commented 3 years ago

Palindrome mode applies from the 3' end of the 'other' sequence, in each case. The 'prefix' sequence of the forward read, which is upstream of the 5' end, will be searched for in reverse-complement, at the 3' end of the reverse read. The 'prefix' sequence of the reverse read, will be searched for at the 3' end of the forward read.