Sequencing Depth (Read Depth) Calculations

Question

[R.L.]

Hi Community,

I have to calculate the read depth of HG002 UCSC Nanopore Sequencing data for my benchmarking.

I downloaded 3 fastq files provided in GIAB and mapped them with minimap2.

minimap2 -ax map-ont --secondary=no --MD

ChatGPT gives me following cmd to calculate:

sequencing_depth=$(samtools depth -a "$sorted_bam_file" | awk '{sum += $3} END {print sum/NR}')

echo "Sequencing Depth: $sequencing_depth"

This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone have a sense on the correctness of this 40x depth?

Thanks a lot

[Pierre Lindenbaum]

it looks looks ok to me.

[R.L.]

Thank u very much!

Answer 1

[GenoMax]

You could also use pandepth (LINK) or mosdepth (LINK) as well. These will allow you to be flexible about windowed coverage etc.

[R.L.]

Understood! Gonna try those two!