What do you mean by " they have no common bases "?

Of course, they do not have common bases, but shouldn't it be like that. Have you read about the double strand DNA and concept of complimentary bands in DNA?

Abhijeet Singh

I mean if the pcr amplicon divides into two it will not have any overlapping in merging process because the half of the sequence is for forward and the another half is for reverse certainly they will never have overlap. So I would like to know how they merge in DNA analyzing data?

In my case, the reads are paired-end. I got lower merging percent in downstream process, but I got curios how it is possible they have overlapping although they merging.

In other words, what is the secret of the sequencing that the paired-end reads must be merged; however, they have no overlapping.

Any idea?

Yes, you are right in this case, they would not overlap. In illumina, you have to trim the reads so you could not get actually read of 240 bp. So the reads would not merge. I you would have done MiSeq run, then they must have overlapped and merged.

Its not secret. its just if the reads are long enough to have the sequence overlap, they they overlap, simple. As in mage.

You can work with only one read, preferably the forward.

Abhijeet Singh

Yes, you are tonally right. I have to use only forward read and to ignore the reverse one.

What factors do impact the reads (f & r) not to merged?

And what will be happened if the reads have no overlapping? Software has strategies for solving the issue?

Thanks

* What factors do impact the reads (f & r) not to merged?

>> If you see the image properly, it is mentioned in bold.

* And what will be happened if the reads have no overlapping?

>> Nothing will happen, you just will have less information (50 %) of your amplicon.

* Software has strategies for solving the issue?

>> If the reads do not overlap, they do not overlap, no software can do that. (there is nevertheless, exception to that, but that is for higher bioinformatics)

Abhijeet Singh

Thanks for the reply.

I have only a small question.

Based on the photo you uploaded, the reads are single stand or double stand?

I thought they are double stands however in the photo it shows they are admittedly single stand. Or in the photo it is symbolic?

If they are single end in reality, it is quite complex to understand. If they are double stands, I back to the my original question because not only in my case, but also never ever they will not have overlapping for other cases!

My question is how possible a read be longer than half of an amplicon although reads (r and f) sequenced equally in an amplicon, to my knowledge? I hope it would be clarified.

I cannot digest it!

Confusing!