Would it be OK if the Read 1 and Read 2 Seq Primer are identical for Myseq?

[nucacidhunter]

Dear Friends,

I am designing a pipeline to construct a 2X250bp Pair End lib for Myseq.
I have identical adapter on both end of my DNA. To avoid the waste of sequencing bases, Would it be OK if the Read 1 and Read 2 Seq Primer are identical?

Best

Identical adapters in both ends will not work because:
1- different adapter sequences are required for clustering and bridge amplification.
2- even if somehow you mange to cluster, during sequencing read1 and read 2 primers are dispensed from different tubes in cartridge and bind to related motif on adapter to prime sequencing. If you library fragments are flanked by P7 or P5 adapters then one of the read primers will not bind to related read primer binding site.

It is not clear what you mean by "avoid waste of sequencing bases".

[mastal]

You would have to use the reverse complement of the sequence for Read2.

[aaron_tao]

Dear Friends,

I am designing a pipeline to construct a 2X250bp Pair End lib for Myseq.
I have identical adapter on both end of my DNA. To avoid the waste of sequencing bases, Would it be OK if the Read 1 and Read 2 Seq Primer are identical?

Best