Question: Do mate 1 and mate 2 reads correspond to the 5' and 3' ends?
0
gravatar for Koustav Pal
9 months ago by
IFOM - FIRC Institute of Molecular Oncology
Koustav Pal0 wrote:

In a paired-end sequencing experiment, a mate pair is generated. Let's call them read 1 and read 2.

For this post, my question is with regards to the various forms of transcriptomic experiments.

When I split the fastq files into the two mates, does the mate 1 always corresponds to the 5' end and mate 2 to the 3' end of the fragment that is sequenced?

I am trying to differentiate between read pairs that came from the sense versus the antisense.

sequencing • 312 views
ADD COMMENTlink written 9 months ago by Koustav Pal0
3
gravatar for genomax
9 months ago by
genomax73k
United States
genomax73k wrote:

mate pair means something specific in high throughput sequencing and refers to long-insert paired-end reads.

When I split the fastq files into the two mates, does the mate 1 always corresponds to the 5' end and mate 2 to the 3' end of the fragment that is sequenced?

R1 is 5'-->3' read from top strand of the fragment being sequenced. R2 is 5'-->3' read from the bottom strand of the fragment being sequenced. Whether they come from the sense or antisense strand will be determined by the library type and the annotation of the gene.

ADD COMMENTlink modified 9 months ago • written 9 months ago by genomax73k
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