I have many reads from antibodies experiments and, to do the experiment, they used many different primers (due to antibodies having a huge variation amongst them) in two different steps of the study (they reamplified the sequences before doing the sequencing). The goal of the study is to make a library of different antibodies and, to do that, I need to find out the primer sequences that may be within the sequences.
I've already used Trimmomatic to remove the adapters and now I'm using nhmmer to identify possible primers within the sequences, but I have two questions:
-Previously I've used hmmscan to find overlapping proteins using the domtblout and filtered by e-value, but there is no such thing in nhmmer (finding domains), so I tried using just tblout, but I couldn't find if using this option would be equivalent to the domain finding process that I've used before.
-After I finish this hmmer part, I was thinking of making a Blast of the Hmmer results to see if they do match with antibodies, do that make sense?
Thanks in advance.
