Get rid of Low Quality Bases In A Sequence, and which be replaced on removed place?

Question

[9521ljh]

if we remove low quality base on read by programming, for example ''sickle'', then what is be replaced on there?

if we put the null value 'N' on there, i think it make big problem for mapping.

For example,

we have sequence

ATCGACTAGATACCCGTT (bold meaning low quality)

and we remove it and it would be

ATCGACTAGATCCCGTT ??????????????

i think it might also make problem for mapping.

Answer 1

[WouterDeCoster]

It is probably not a good idea to remove or replace nucleotides in a read.

If anything, you could decide to stop the read there:

ATCGACTAGATACCCGTT becomes
ATCGACTAGAT

This is called 'trimming'