Prokayrote genome coverage help

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Hi, I would like to know my genome coverage from FASTQ file. I use glaxy.org to generate SAM then BAM . Finally I got multibam summary. I download file for each stage but I got the file that’s not human readable.

How will I get the genome coverage information e.g 12X

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Hi @petermyintzaw,
you can use the bedtools Genome Coverage tool for computing the coverage of each nucleotide. It is important to set as yes the option Report regions with zero coverage in the bedtools Genome coverage tool (otherwise the regions with coverage = 0 won’t be included). Finally you can use the datamash tool for calculating the average coverage for the whole genome.

Regards

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Hi @gallardoalba @petermyintzaw could you help me with some more information in coverage calculation please?

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@dna please ask your question directly and maybe open another question.

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@bjoern.gruening thanks for your suggestion. I have the raw R1 and R2 files of a bacterial genome sequence and their contig-assembly by spades. How can I calculate the genome coverage / depth? Thanks.

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If this is a de-novo assembly the interesting questions are what is your N50 or L50 etc, please read more about that here: An Introduction to Genome Assembly

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@bjoern.gruening thanks again! N50 is 34120, l50 is 20.

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