capture hash UMI counts for non polyA hashes

[eliza-barkan]

Would it be possible to capture hashes that do not have a polyA tail (i.e. some specific sequence instead)?

Thanks!

[hpliner]

Currently the script looks for AAAA in positions 11:15 of the read. Would the alternative be something similar? I.e. a sequence in a specific position?

[eliza-barkan]

Yes, maybe there could be two options where the default is polyA or you can input a custom sequence and specify at which positions to look for the sequence at