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nucacidhunter · 02-20-2019, 06:27 PM

I assume you have done PCR wit ITS region specific primers with no Illumina overhang or full adapter sequences. In this case they must have prepared library by adapter ligation which will result in non-direction library so R1 and R2 can start for some fragments from forward direction and for others from reverse direction.

You should check some reads from R1 and R2 sequence folders and you should see in both sequences starting with forward and reverse primers, unless they have been sequenced with custom primers or have been trimmed to remove PCR primers.

02-20-2019, 06:27 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	I assume you have done PCR wit ITS region specific primers with no Illumina overhang or full adapter sequences. In this case they must have prepared library by adapter ligation which will result in non-direction library so R1 and R2 can start for some fragments from forward direction and for others from reverse direction. You should check some reads from R1 and R2 sequence folders and you should see in both sequences starting with forward and reverse primers, unless they have been sequenced with custom primers or have been trimmed to remove PCR primers.