I have a library of plamids that looks like this (plasmid_top...INSERT... plasmid_bottom) since the plasmid_top is more than 1000 b long i decided to look only for 30 base adjacent to the insert (i added in adapter.py file 30 base long adapter/identifiers).
i am confused on whether it will treat these as middle adapter and split the read or discard them. see below
under "Barcode demultiplexing" it is stated :
Note that the --discard_middle option is always active when demultiplexing barcoded reads. This is because a read with a middle adapter is likely chimeric and the pieces of chimeric reads may belong in separate bins.
but under the "Full usage" it is stated:
(default: split reads when an adapter is found in the middle)
so i am a bit confused since it always demultiplexes does Porechop discard reads with middle adapters or does it split them....?
I have a library of plamids that looks like this (plasmid_top...INSERT... plasmid_bottom) since the plasmid_top is more than 1000 b long i decided to look only for 30 base adjacent to the insert (i added in adapter.py file 30 base long adapter/identifiers).
i am confused on whether it will treat these as middle adapter and split the read or discard them. see below
under "Barcode demultiplexing" it is stated :
Note that the --discard_middle option is always active when demultiplexing barcoded reads. This is because a read with a middle adapter is likely chimeric and the pieces of chimeric reads may belong in separate bins.
but under the "Full usage" it is stated:
(default: split reads when an adapter is found in the middle)
so i am a bit confused since it always demultiplexes does Porechop discard reads with middle adapters or does it split them....?