Trinity assembly and qPCR

Vinn · 07-11-2016, 05:03 AM

Hi folks,

I have new RNAseq data assembled with Trinity, and now I am trying to use qPCR for validation. I blasted a gene of interest from another species against the RNAseq data for primer design, but I have got something like this in return.

comp82676_c0_seq1
comp82676_c0_seq2
comp82676_c0_seq3
comp82676_c0_seq4
comp82676_c0_seq5

All of them are best hits and have identical score and E value. They only have tiny gap differences when I aligned them.

May you explain what are diffrences between them and which one I shall use for primer design? I want a primer to amplify both gene of interest and the closest hit from the new RNAseq data.

Thank you very much for your time and help!

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07-11-2016, 05:03 AM	#1
Vinn Member Location: Sweden Join Date: Nov 2014 Posts: 18	Trinity assembly and qPCR Hi folks, I have new RNAseq data assembled with Trinity, and now I am trying to use qPCR for validation. I blasted a gene of interest from another species against the RNAseq data for primer design, but I have got something like this in return. comp82676_c0_seq1 comp82676_c0_seq2 comp82676_c0_seq3 comp82676_c0_seq4 comp82676_c0_seq5 All of them are best hits and have identical score and E value. They only have tiny gap differences when I aligned them. May you explain what are diffrences between them and which one I shall use for primer design? I want a primer to amplify both gene of interest and the closest hit from the new RNAseq data. Thank you very much for your time and help!