Identity matching for each sample and for each analysis was performed by extracting genotypes from PCHi-C and ChIP-seq and comparing them to SNPs from the WGS data. The first stage of verifying the sample identity concordance between the ChIP-seq and WGS data involved pre-processing the BAM files for one autosomal chromosome (chr1) to remove PCR duplicates and reads with mapping quality score <10. The variants were then called from the resulting BAM file using mpileup from the SAMtools package77. The variants with QUAL < 20, DP < 5 and GQ < 5 were filtered out. Then, we compared genotypes of the filtered variants with genotypes generated from WGS and imputation. The genotypes generated were considered to be from the same sample if the concordance rate was greater than 90%.

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.