Threshold Quality Default Number

Question

[vitorgomesbio]

I just want to know why the default value for the LEADING: Cut bases off the start of a read, if below a threshold quality and TRAILING: Cut bases off the end of a read, if below a threshold quality is 3. What happens if I change this number? Where I can find some information about base quality?

Answer 1

[finswimmer]

Hello,

the base quality values are also called Phred quality score, and gives you the probability that a base is called incorrectly. The higher the number the more you can be sure that the base is correct.

In the first years after NGS arises (especially by illumina) one saw a significant drop off of the base quality to the end of the reads. That's why it was common to cut those bases, because wrong called bases had influence on the mapping/alignment/assembly. These days this drop off isn't that critical anymore and quality trimming can be omit in most cases.

fin swimmer