How much sequencing coverage do you need in order to detect SNP's across the whole genome
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3.1 years ago
dk0319 ▴ 70

I am developing a project that would utilize either SNP detection, ChIP-seq, Cut and run, or potentially a combination of these techniques. I am interested in knowing what the current recommended coverage is for SNP identification in human cell culture. Similarly, I am really interested to hear how coverage for SNP analysis compares to ChIP-seq and Cut and Run. Any additional info regarding cost comparisons would also be extremely useful.

sequencing SNP ChIP-Seq next-gen • 551 views
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Are you exclusively interested in SNPs at loci that bind a protein or have a certain histone modification? ChIP-seq is usually done with 20-50mio reads, CnR with like 5mio reads, and sequencing for SNPs strongly depends on the type of sequencing (exome, WGS) and the amount of money you can spend. Please add some details as I do not see the connection between SNPs and ChIP/CnR yet.

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I am interested in detecting any SNPs in the genome. The SNP approach would involve WGS and there would be no enrichment step like TF/His Chip. So I recognize I will need far more coverage, and as such pricing becomes a major issue. Ideally I would like to find a reasonable lower limit that would permit for replicates.

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