How to determine X depth of raw reads (FASTQ files)

Question

[hashish]

Dear All, Please, may someone help me how to determine the X depth of raw reads (FASTQ) files generated from MiSeq? Using any windows-based or web-based tool. " I have no idea how to use the command line" Thank you,

Answer 1

[Pierre Lindenbaum]

I'm afraid you'll have to map the reads on a reference genome, and then extract the DEPTH (Tools To Calculate Average Coverage For A Bam File? )

Using any windows-based or web-based tool. " I have no idea how to use the command line"

It's always a bad idea to use a non-command line tool (automatization, speed, reproducibility ...). Anyway you can always try CLC Workbench or https://usegalaxy.org/ , etc...