I have sequences from 6 bacterias (E. Coli and Salmonella). 6 samples have been sequenced using PacBio on 4 movies so I have 3 bax files for every movie (12 in total).
I converted bax file to bam using Bax2Bam and then I used Lima to do demultplexing (using a set of about 330 barcodes in fasta). The output of Lima = 4 bam files (= number of movie).
The question is, how can I filter/split that file by sample? I would like to get 6 file - each for every sample.
Thank you in advance.