How to deal with the Ns in gene sequences?

Question

[lakshmi.bioinformatics]

I have around 30 k sequences and need to find the codon frequencies how to deal with the presence of Ns in the sequence

Should I need to mask the regions or to replace with specific nucleotides or try any other methods to overcome this issue? Will this manipulate my results?

[Ram]

I'd recommend masking these regions.

[lakshmi.bioinformatics]

How to mask using Python program

[Ram]

Why use a Python program? Is this an assignment question?

[st.ph.n]

These are NGS reads?

[lakshmi.bioinformatics]

These are gene sequences retrieved from Ensembl database

[st.ph.n]

Is it fasta format then? If this is an assignment, can you use biopython?

[lakshmi.bioinformatics]

Yes the sequence is in fasta format and how to mask with biopython also I need to draw a CGR how can it be done with biopython