Hi,
I'm working on Illumina short paired-end reads of human genome and when I do BLAT on short reads, I'm seeing that not all read /1's are from one strand. e.g. here is what I got for my first 5 paired-reads:
Read# R1 R2
(1) - +
(2) + -
(3) + -
(4) + -
(5) - +
...
So, my question is: regardless of reads orientation, is there any rule that first read is always coming from one strand and Read 2 from the other one in Illumina sequencing? I was assuming this but it seems that its not true.
I appreciate if anybody can comment on this.
I'm working on Illumina short paired-end reads of human genome and when I do BLAT on short reads, I'm seeing that not all read /1's are from one strand. e.g. here is what I got for my first 5 paired-reads:
Read# R1 R2
(1) - +
(2) + -
(3) + -
(4) + -
(5) - +
...
So, my question is: regardless of reads orientation, is there any rule that first read is always coming from one strand and Read 2 from the other one in Illumina sequencing? I was assuming this but it seems that its not true.
I appreciate if anybody can comment on this.
Comment