Is there any script on how to check the depth of the sequencing region on my Mac terminal?

Question

[nudrylab]

Hello, I am trying to find a script that can help me check the depth of sequencing of the region. I want to see if the particular region was sequenced in all areas or is it different. Whole-exome sequencing FastQ file.

Thank you

[GenoMax]

There is a program called mosdepth (LINK) that will fit the bill. Install using conda.

Answer 1

[ATpoint]

Fastq files first have to be aligned to the genome, then you may apply mosdepth or something like samtools depth. Alignment software could be bwa mem or bowtie2 among other choices. Please google for popular alignment tools or read previous posts on that topic here. Since fastq files only contain the raw sequences without positional information you cannot quickly check any region from those files, and before you ask, no you cannot align against only the region you are interested in, it must be the entire genome that the WGS was based on to avoid false alignments.