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jordiabante / CpelAsm.jl

Julia module to perform haplotype allele-specific DNA methylation analysis.
https://jordiabante.github.io/CpelAsm.jl/dev/
MIT License
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The calculation results seem to have issues #10

Closed sjbxzpf closed 7 months ago

sjbxzpf commented 10 months ago

Dear CpelAsm Team, I have followed your instructions to calculate the results, but they seem to lack statistical significance, and the p-values are close to 1. I cannot identify where the issue might be. Do you know what could be causing this situation? I really hope to receive your assistance. 1703425833761

sjbxzpf commented 10 months ago

To facilitate pointing out my issues, I will briefly describe the processing pipeline:

  1. WGBS data undergoes Bismark alignment.
  2. BS-Snper identifies SNPs.
  3. WhatsHap utilizes WGBS data for SNP phasing (this step may have implications for subsequent analyses due to the lack of WGS data).
  4. Creating an N-marked genome with heterozygous SNPs.
  5. Re-aligning WGBS data to the N-marked genome using Bismark.
  6. Using SNPSplit to separate reference and SNP alleles. SNPs in the forms 1|0 and 0|1 are separated, and 1 (1|0) + 0 (0|1) are combined into a1, while 0 (1|0) + 1 (0|1) are combined into a2. The unassigned.bam is obtained from the phased SNPs.
  7. VCF containing only heterozygous SNPs.
  8. Running the analysis using run_analysis(a1, a2, unassigned.bam, vcf, fa).

I also have a question: What is the role of homozygous SNP? Are they used to modify the reference genome? thanks