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Old 11-15-2017, 03:26 PM   #1
Immunity
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Default Targeted RNASeq procotols for viral sequencing

Hello,

I am starting a project on which I would like to detect viral RNA (herpes) in human tissue. Essentially I would extract the RNA, perform targeted amplification and library prep for multiple viruses and then sequence. I think I have an idea of the bioinformatic system to use.
However, I am not really sure where to start on the library prep issue (i.e. which library prep system to use). I've looked into ScripSeq which sounded promising but seems very expensive.

Is there a "custom" protocol/template out there than I can use to accomplish these goals. My main concerns are (if i would to start with known herpes primers, how would I successfully make a library that contain adapters and index for multiplex?)

Thank you and excuse my naive questions. I am not new to using NGS for already commercially prepared custom gene panels (i.e. Qiagen targeted RNASeq panels) but I am new in developing custom assays so your help would be greatly appreciated.
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Old 11-17-2017, 03:33 PM   #2
Immunity
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I found out what I needed if anyone is interested. It is called (16S Metagenomic sequencing library preparation). It is made for 16S rRNA targeted amplification, however the protocol can easily be adjusted for any targeted region on any genome. all you need is to attach illumina adapter overhang sequences to the targeting Forward and Reverse primers, amplify, clean up, amplify again with indexes, clean up and sequence.
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