inner and outer genomic coordinates concept

Question

[seta]

Hi everybody,

Could you please kindly tell me what is the meaning and concept of outer in the below sentence? so sorry if you found the question is a basic, but I have to ask.

Toolkits for aligned reads use the outer genomic mapping coordinates of paired-end reads as an indication of identical fragments.

Thank you,

Answer 1

[h.mon]

Do you even google your question before posting it? There are two answers here, to the exact same question, which arose from reading the exact same passage of the exact same book you are reading.

[seta]

Of course, google is the first one. To be honest, I saw the link, but unfortunately didn't get the point of interest. I'm looking for an image for understanding outer and inner genomic mapping coordinate, my problem is the concept of outer and inner, here, not detecting duplicates by mapping.

[h.mon]

• Outer: coordinates of 5' side of R1 and R2
• Inner: coordinates of 3' side of R1 and R2

This definition holds for standard paired-end Illumina libraries, where DNAseq reads should map with a FR orientation. For other technologies and / or read orientations, honestly I don't know.

As adapter and quality trimming generally removes bases from 3', and when people do 5' trimming is generally a fixed number of bases, outer coordinates are better to find duplicates.

[seta]

Thank you very much, h.mon