Please delete this thread - I found out the problem, but thanks to reading the other thread. Apologies for the posting!
Sorry, I kept searching (changing the words) and find a thread that only drops those that aligns beyond the reference? Is that the case?
You want to keep the bases that don’t align to the reference? As in start before or go beyond the end of the alignment? As a work around, you could add a bunch of . to the beginning and end of the alignment.
This is a dataset I received from a larger project, and sequencing is run by one of the PI’s team. I didn’t realize they had used a different sequencing approach to what I do in my other projects (e.g. the one I used for the fish project at MARS). So the primers are in the sequenced region - an oversight from my side. So it is fine - the lost of bases is the trimming of the primers at the alignment step, that is actually pretty clean.
Lesson learned - always check what protocol is used for lib prep and sequencing if you do not do it yourself…
ack!! good luck with dealing with that. Working with others data is always an adventure.