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

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,

next-gen genome depth
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by hashish • hashish

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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...

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written by Pierre Lindenbaum Pierre Lindenbaum

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