I need to get the fold-coverage
Hello by what tool I know the genome coverage (X) of assembly contigs. Thank you
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dungnv114 •
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kamel •
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kamel •
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Thank you for your reply. but I can't use the calculated theoretical C = R x L / G, because I have the reads length 32-250 (so it is not a single value) and I can't use bedtools because I want to know the fold-covrage from assembly of Novo result (not from mapping).
If you want to know the coverage of your denovo assembly you could try mapping the reads to your assembly and then calculating coverage as suggested by the following answers. A not-so-correct way is to see how much of data you have (in total bases) in your assembly and use this as the denominator to divide the total data you have (i.e in place of G in the above formula). This post might help - Counting Number Of Bases In A Fastq File
But you would obviously be over-expecting coverage since there would be missing data due to a fragmented assembly. So you definitely need to map back your reads to your contigs (keeping these as a reference) to understand how much of coverage you might have.