illumina: Adapter Confusion

Question

[lingjun meng]

When learning about NGS library construction,I have a problem:

Library is automatically denatured into single strands and further diluted onboard the instrument.

It feels like double strands are used as input,and we may get two reads representing the same fragment.

A typical library like this:

After pcr,it seems like:

So are both the black forward strand and the gray reverse strand sequenced? Will it cause any problem?

[lingjun meng]

Cant edit answer because of the great fire wall

Answer 1

[lieven.sterck]

unless you are using a strand specific protocol (very common nowadays, perhaps even default now) , both strands will be sequenced.

In general this will not cause any problems for downstream analyses. This situation is usually 'resolved' by for instance the read mapping software. Most of the times reads mapping to the sense or anti-sense of a locus are simply "grouped" to get an end result (eg in gene expression analysis).

[GenoMax]

Even for regular libraries, aligners will report alignments (if they are on the bottom strand) using appropriate SAM flags.