Count all (non N) nucleotides within regions defined in BED file

Question

[William]

Is there an easy way with some tool or library to count all (non N) nucleotides within regions defined in BED file?

Of course in combination with the reference genome fasta on which the regions are defined.

This to check that all (non N) nucleotides of the reference fasta are in 1 region of the BED file?

Answer 1

[Prasad]

You can extract sequences for bed regions using "getfasta" followed by base counting using any of the options provided here

[William]

Thank you. I'll use the pyfastx fasta composition to compare the content of the getfasta and original fasta file. Also added that option to the linked question.