This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Get rid of Low Quality Bases In A Sequence, and which be replaced on removed place?

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
• 884 views • link
updated by WouterDeCoster WouterDeCoster • written by 9521ljh • 9521ljh

1 answer

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'

• 0 views • link
written by WouterDeCoster WouterDeCoster

Log in to answer this question.

More posts like this