I think I am having trouble understanding PCR and trimming tools. After amplification using forward and reverse primers in PCR, wouldn't the resulting strands include forward primer, reverse primer, reverse-complementary forward primer and reverse-complementary reverse primer?
from the original antisense DNA strand (3' -> 5') for instance, PCR will result in:
5' forward primer ..... DNA sequences .... complementary of reverse primer 3'
3' complementary forward primer .... complementary DNA sequences .... reverse primer 5'
I have got reads from PacBio (single-end library), and I assume the sequences are from 5' to 3'. Then, does this mean that the amplified 3'->5' strand will be reverse in the reads, resulting in the reverse primers too? For instance, complementary forward primer -> reverse-complementary forward primer?
If I were to trim the forward primer using a software, will this also detect complementary forward primer and reverse-complementary forward primer sequences?
Thank you in advance!!