Questions tagged [qc]

Quality Check or Quality Control. The assessment of the quality of a product, data. For example, in sequencing data, the assessment of the quality of the bases. QC can also include the pre-processing of data to make it attain minimum quality requirements.

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What is the best QC to do on imputed UK Biobank data?

I am receiving imputed data from UK Biobank to conduct a GWAS on. Previously I have carried out GWAS on genotype data, which I have QC'd for missingness per individual and per SNP, sex discrepancy, ...
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Help with Seurat QC ambiguity

I have four PBMC samples from 10X scRNA-seq ...
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146 views

Oxford nanopore promethion; does guppy3 separate fast5 into pass and fail? If not what does?

just a quick question about fast5 pass fail folders. I have been working under the assumption that the fast5 pass fail folders I was given as raw data from our ONT vendor came from them doing base ...
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nanopore QC measures on fastq file

I am working with virus nanopore sequencing data. I have to remove host genome from the reads. I want to run the QC on the fastq file after host genome subtraction. I have used nanoplot. It is slow. I ...
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208 views

Interpreting MultiQC plot of GATK BaseRecalibration data?

I'm using GATK4 to build a somatic variant calling pipeline. The pipeline uses MultiQC to aggregate quality control data, and one of the QC measures reported is base quality score recalibration from ...
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Common QC parameters and threshold in human WGS pipeline

I am trying to summarize a list of QC-parameters and its threshold that should be applied for human WGS in general to avoid bad quality of data. Which qc parameters for WGS are you using and why? ...
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232 views

RSeQC provided bedfile does not work with read_distribution.py

I frequently make use of RSeQC, I used to use it with my own bed file, generated using gtf2bed, but now I thought I'd use the one provided by RSeQC themselves from here, I got the file ...
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Why does cutadapt remove low quality bases from the ends of reads only?

I use cutadapt to remove low quality bases from my Illumina reads. The algorithm only removes low quality bases from the end until it reaches a good quality base. If there is a bad quality base beyond ...
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178 views

What sequencing data metrics should I record?

I'm new to bioinformatics and Im starting a new microbial sequencing project and I'd like to record all of the qc data correctly. This is research and I'm not sure what I'll need later. Is there any ...
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Filtering imputed GWAS SNPs based on a MAF difference of 10%

There are many posts on the web regarding QC steps pre and post-imputation. Does applying below (new?) 10% MAF difference rule make sense, pitfalls? Here is the process: Get MAF for imputed set, ...