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
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