Questions tagged [quality-control]

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Help with 1D^2 library shearing

I've done my 1st trial of 1D^2 whole genome sequencing using LSK-SQK308 kit with R9.5 flowcell. Without doing library fragmentation, I encountered the unexpected library shearing during sequencing. ...
3
votes
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99 views

Remove variants that do not map to human genome

I received an hg38 VCF file that's had variants imputed with 1000 genomes. I've encountered some issues with the VCF; REF alleles that do not align to a reference genome, ALT alleles that do not ...
0
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Common QC parameters for SNP chip data in PLINK

How do you set QC measurements? Seems very subjective. Is there a right way to set: 1) individual call rate, 2) SNP call rate, 3) minor allele frequency (MAF), and 4) linkage disequilibrium (LD) in ...
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Quality checking benchmarks for clustering

I'm currently working with several RNAseq datasets from the ENCODE database. My approach to assessing the quality of the data, i.e, reproducibility is by automating the assessment of expression ...