DNA Ghost:

This note based blog covers bioinformatics and cancer genomics 

January 23, 2018

We may occasionally find unexpected amount of poly-G reads in raw data generated from NextSeq. See FASTQC figure below as a typical example. 

In the figure of k-mer content, all kinds of G-enriched k-mer peeks almost throughout the reads. The poly-G probably also s...

November 25, 2017

Note that the statistics we are going to talk about only applies to germline mutation, not somatic mutation.

Once we called a list of SNPs. it is routine that we get some statistics out of them. These statistics commonly include:

Transition / Transversion (Ti / Tv) rati...

August 25, 2017

Roughly, RNA-Seq may have the following bias sources:

  • Random priming

  • PolyA selection (3’ bias) and ribosomal depletion

  • PCR duplicates

  • Normal cell contamination (when evaluating tumor)

  • Tumor purity

  • Batch effect

Random priming

Appears at firs...

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