Is it normal to have NGS paired read data to be complementary?

[balaram26]

Hi,

I am new to NGS data analysis. I have got NGS read data from the Demo run. The Data is from HLA typing using NGS Technology. On looking the read data obtained, the Read 1 and read 2 data where completely complementary to each other. Is it normal ?? I have read that the Paired reads produced by NGS usually overlaps in the 3' region. But can the whole read 1 and read 2 be complementary to each other?

The data was generated using Illumina sequencer. I had read 1 and read 2 in separate files. The read lengths was around 150 bp each. I am not aware of the illumina sequencer details.

[Heisman]

If you have a fragment that is less than 150bp sequenced, then the entire fragment will be sequenced from each end; this may be what you are seeing. However, when this occurs the read goes into the adapter sequence. If you are not seeing adapter sequence, perhaps it was trimmed off before the reads you are looking at now. However (again), if that occurred, it would be very unlikely that the reads would be exactly 150bp.

Could you maybe post an example of a complementary read that you are seeing? Or maybe a couple of examples?

[balaram26]

Thanks for the reply. I checked the small reads,only they are complementary. the big ones are not complementary. In this case,how to process these small reads?

[GenoMax]

Thanks for the reply. I checked the small reads,only they are complementary. the big ones are not complementary. In this case,how to process these small reads?

Can you clarify what you mean by "big" and "small" reads? Is that referring to read lengths?

Have a look at this thread (and links contained in there): http://seqanswers.com/forums/showthread.php?t=32005

There are several suggestions for software that can process overlapping reads and then compress them into a single sequence. If your inserts are very small then depending on the read lengths you may have adapters on both ends of the reads. You will want to look at the solution JamieHeather used in the above thread in addition to using software such as FLASH.