Sequencing | DNA Ghost | United States

DNA Ghost:

This note based blog covers bioinformatics and cancer genomics

Recent Posts

Archive

Tags

Variant frequency, effect size and GWAS limitation

Variant frequency, effect size and GWAS limitation

Figure below very well explains two important attributes of a variant: population frequency (to avoid confusion, we use "population frequency" instead of "allele frequency".) and effect size. Evolution dictates that variant's population frequency is generally inversely proportional to its effect size. To detect significant association between a variant and specific phenotype, the variant has to meet either one of two prerequisites: The variant has to have at least modest popu

Selectively talk about some scenario you may see in FASTQC report

Selectively talk about some scenario you may see in FASTQC report

Um... interesting plot below it is. I believes you all sew all sorts of wired pictures time to time. I wanna bring some sections into spotlight and talk about it. Caveat: pass / failure criteria of FASTQC is specifically designed for DNA-Seq. Some sequencing (RNA-Seq, targeted sequencing or 16S) naturally have uneven proportion of duplicate reads and bias. This may cause false positive failure in: Per base sequence content Per sequence GC content Sequence duplication levels P

GET IN TOUCH