We start most BCR/TCR repertoire analyses using HTSeq data by removing the primers (forward and reverse in paired-end-sequencing) and adapters. However, sometimes the primer sequences are not known (e.g. not provided by the company that sells the kit). Moreover, the number of used primers and their lengths might also be unknown.
Have you encountered such an issue before, and is there a tool/pipeline for computational primer identification directly from the data?
Best