Hi, I have used ONT minimap to align combined reference sequences (fasta file combined together in one file but separated by header " >" for each reference sequence). Then, I got one aligned sam file . My question is I dont know how to filter out my aligned data to each of the reference sequence. Details are below:
I have 2 reference sequences in fasta format (lets call it A and B)
And one aligned data in sam format.
I want to see how many sequences align to each referenec DNA sequence (A and B)

Do I use the awk comand

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