Get rid of Low Quality Bases In A Sequence, and which be replaced on removed place?
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1
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3.4 years ago
9521ljh ▴ 50

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.

rna-seq snp sequence sequencing • 450 views
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2
Entering edit mode
3.4 years ago

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'

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