Hello there,
I want to know if there is any way to calculate the coverage at a specific nucleotide across the amplicon using the average coverage, with the assumption that the reads are normally distributed across the ampliocn.
Say I have sequenced a 1.3kb amplicon, with read length 300 nts, and number of reads 10000. using Lander/Waterman equation (LN/G), the average coverage will be ~2300x. This tells us that every nucleotide was covered at least with 2300 reads. My question is that, can I estimate roughly the actual number of reads cover a certain nucleotide across the ampliocn, say nucleotide number 9, or any other nucleotide. Is it doable in a theoretical way without using tools like bedtools or samtools?
Many thanks
I want to know if there is any way to calculate the coverage at a specific nucleotide across the amplicon using the average coverage, with the assumption that the reads are normally distributed across the ampliocn.
Say I have sequenced a 1.3kb amplicon, with read length 300 nts, and number of reads 10000. using Lander/Waterman equation (LN/G), the average coverage will be ~2300x. This tells us that every nucleotide was covered at least with 2300 reads. My question is that, can I estimate roughly the actual number of reads cover a certain nucleotide across the ampliocn, say nucleotide number 9, or any other nucleotide. Is it doable in a theoretical way without using tools like bedtools or samtools?
Many thanks
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