Question on nanopore sequencing data process pipeline (cDNA-PCR)
I recommend that you look at the most recent version of the protocol, which includes example adapter and barcode files:

https://www.protocols.io/view/stranded-mapping-from-long-reads-syheft6?step=2

[check in the protocol to see if there's a more recent version]

These files contains the public sequences that ONT have released for their sequencing kits (as briefly mentioned in the "Before Starting" section of the protocol). The sequences are available on the ONT community, but I have converted them into FASTA files for use in my protocol.

The adapter and barcode files were combined into a single FASTA file in the previous version of my protocol. For the PCR cDNA barcoding, it looked something like this:

&gt;ONT_VNP
ACTTGCCTGTCGCTCTATCTTCTTTTT
&gt;ONT_SSP
TTTCTGTTGGTGCTGATATTGCTGCCATTACGGCCGGG
&gt;BC01
AAGAAAGTTGTCGGTGTCTTTGTG
&gt;BC02
TCGATTCCGTTTGTAGTCGTCTGT
&gt;BC03
GAGTCTTGTGTCCCAGTTACCAGG
&gt;BC04
TTCGGATTCTATCGTGTTTCCCTA
&gt;BC05
CTTGTCCAGGGTTTGTGTAACCTT
&gt;BC06
TTCTCGCAAAGGCAGAAAGTAGTC
&gt;BC07
GTGTTACCGTGGGAATGAATCCTT
&gt;BC08
TTCAGGGAACAAACCAAGTTACGT
&gt;BC09
AACTAGGCACAGCGAGTCTTGGTT
&gt;BC10
AAGCGTTGAAACCTTTGTCCTCTC
&gt;BC11
GTTTCATCTATCGGAGGGAATGGA
&gt;BC12
CAGGTAGAAAGAAGCAGAATCGGA
&gt;RB12A
GTTGAGTTACAAAGCACCGATCAG


I separate out adapters and barcodes in the newer versions of the protocol because I was getting too many incorrect hits.