Extension of reads

Question

[madhu.9124]

Hi,

I just want to extend the read by 20bp to the 3' or 5' end of the read, with high quality score, based on the reference genome sequence. Kindly suggest command or tool for doing it.

Answer 1

[Brian Bushnell]

BBMap does not do reference-based extension, but you can do coverage-based extension like this:

tadpole.sh in=reads.fq out=extended.fq el=20 er=20 mode=extend k=62

[madhu.9124]

thanks, is there any tool which can do reference based extension. How do i also extend with high quality score?

[Brian Bushnell]

I don't know of a tool like that.

The quality score Tadpole assigns for extension is arbitrary; I think it's Q30.

[GenoMax]

How do i also extend with high quality score?

Why are you so interested in getting high quality scores on the alignment (considering questions you have posted so far)? We generally want high Q scores for raw data.

[madhu.9124]

I am testing BBmap application and the requirement says high quality score.

[Brian Bushnell]

What requirement are you talking about?

[madhu.9124]

the functional requirement to test the application.