I read the page and get to know Paried end reads are most oriented to the NGS, like Illumina aiming to get longer sequencing read.
But (anything gets a but), I received data set from Sanger sequencer. For each read, they have both forward and reverse reads (aka, paried-end).
From what I read, paired reads are basically:
fragment ================================
fragment + adaptors ~~~================================~~~
SE read --------->
PE reads R1---------> <---------R2
unknown gap .........................................
But after alignment, my one looks like in the following img, they have some region in common
![](https://dl.dropboxusercontent.com/u/24879560/paired-end.PNG)
Anyone knows why they are quite diff? thx
But (anything gets a but), I received data set from Sanger sequencer. For each read, they have both forward and reverse reads (aka, paried-end).
From what I read, paired reads are basically:
fragment ================================
fragment + adaptors ~~~================================~~~
SE read --------->
PE reads R1---------> <---------R2
unknown gap .........................................
But after alignment, my one looks like in the following img, they have some region in common
Anyone knows why they are quite diff? thx
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