We’re rewarding the question askers & reputations are being recalculated! Read more.

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.

Filter by
Sorted by
Tagged with
0
votes
2answers
31 views

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? ...
2
votes
1answer
41 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 ...
8
votes
3answers
661 views

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 ...
3
votes
1answer
122 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 ...
6
votes
1answer
156 views

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, ...