Hello,
I want to know the genome coverage for my wgs of bacteria. I have my 2 raw fastq files and that’s genome’s fasta file as well. But i don’t know how to get the info? please help!
Hi @S_K_A
You can use a tool like → bedtools Genome Coverage
Do QA steps on the reads first, then map them, then run that tool.
The Quality Control and Mapping tutorials here can get you started
If you are brand new to Galaxy, consider running through an Introduction tutorial as your very first step!
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Thank you, @jennaj for the suggestion. I got the result from using bedtools Genome Coverage. However, I can’t analyse genome coverage from these. Does the genome show me sequence coverage? But in the example it’s written " 2. Coverage depth" so will it be the 2nd one after genome or how should I interpret BedCov tool output?
Hi @S_K_A
The coverage from that tool is how deep the reads at each genomic position are.
There are a few ways to do this. What is your larger goal?
Finding out Genome Coverage for the NCBI submission.
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Hi @S_K_A
Would you please share a link to the submission guide you are following? If the guide has several options, please clarify which you are doing. We can maybe suggest the right tool.