<p>I have .fastq files from a targeted amplicon sequencing by Illumina MiSeq run. I want to get the target sequences to perform Blast search on them. What is the pipeline to use for processing amplicon sequencing data? I also have 20% PhiX. </p>

CC BY-SA 4.0
2019-01-11T02:50:28.590Z
Usually you have the targeted regions based on the library/ panel design prior to sequencing.  Do you not have that information?  It is standard Illumina processing to remove the PhiX reads before creating the FASTQs
Bioathlete
CC BY-SA 4.0
2019-01-11T05:56:31.317Z
This is crossposted on biostars: https://www.biostars.org/p/357824/
finswimmer
CC BY-SA 4.0
2019-01-15T17:52:23.350Z
Do you want the reads that contain the amplicon? If you know the primer sequences you could do this pretty easily
d_kennetz
<ngs>
amplicon sequencing set up
# amplicon sequencing set up

(Asked by: username_0 on 2019-01-11)

I have .fastq files from a targeted amplicon sequencing by Illumina MiSeq run. I want to get the target sequences to perform Blast search on them. What is the pipeline to use for processing amplicon sequencing data? I also have 20% PhiX.

**Tags:** ngs
> **Comments:**
> **username_1**: Usually you have the targeted regions based on the library/ panel design prior to sequencing.  Do you not have that information?  It is standard Illumina processing to remove the PhiX reads before creating the FASTQs  
> **username_2**: This is crossposted on biostars: https://www.biostars.org/p/357824/  
> **username_3**: Do you want the reads that contain the amplicon? If you know the primer sequences you could do this pretty easily  

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## 0 answers

