What is the exact definition for per-base count in high-throughput sequencing like ChIP-seq, DNase-seq? If one read is of length 20, this read will be counted 20 times for each base covered? I am new to Bioinformatics and Biostars. I searched on the platform, but didn't find answers. Could you please help? Thanks!
I came across this term "per-base count" from this paper, which indicates there is a per-base count c_i for each base i.
1 answer
Indeed, isn't it strange that one can publish a paper on how to correct per base counts without ever defining what per base count actually is.
In CHIP-seq some people only use 5' ends of reads but for RNA-Seq everyone uses the full read so your guess of the definition of per-base-readcount is correct.
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Istvan Albert
It means the rightmost base of the template, 5' end of a read on the positive strand and 3' end of a read on the reverse strand.
Basically to try to reconstruct the borders of the original DNA template.
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Istvan Albert
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