Entering edit mode
3 months ago
R.L.
•
0
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
it looks looks ok to me.
Thank u very much!