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Old 02-20-2019, 04:09 PM   #1
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Location: US

Join Date: Apr 2013
Posts: 222
Default MiSeq amplicon sequencing Primers?

Hi guys,

I sent some soil samples to a commercial sequencing center. I do fungal ITS sequencing (300bpX 2 paired-end) Miseq.

As you know, I use forward and reversed primers when I did PCR. I suppose Paired-end means sequencing twice, right? I suppose they should use forward primers to sequence once and reverse primer to sequence from another time.

However, I received two mapping files from sequencing center. Both mapping file show they only used forward primer? I am wondering if this is normal?

I know in our forward primer always better and accurate. Back to old days (Sanger sequencing) we only use forward primers to run sequencing reactions.

If you guys are familiar with paired-end amplicon sequencing, I am wondering if it is normal to use only one primer to sequence both (paired).

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