Hi I am currently attempted to understand how pair end sequencing works. I understand the basics that it sequences from both ends and if there is an overlapping region they can be joined to create longer single reads.
From my understanding would the example below be true, please tell me if it is or isnt.
Example:
So essentially the total seq is the whole of the fragement. This is pair end sequenced providing a forward read (seq1) and a reverse read (seq2). However seq2 will be the complement to seq1 due to way the sequencing occurs.
50 A, 50 C, 50 G
TotalSeq = ' AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG'
So seq1 will be sequenced:
----------------------------------------------------------------------------------------------------->
and seq2 will be sequenced: <-----------------------------------------------------------------------------------------------------
This provides an area of overlap which will be the site of matching and merging.50 A, 50 C, 1 Gseq1 = ' AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCG'1 T, 50 G, 50 C
seq2 = 'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGT'
Any help would be ...