Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-11T02:50:28.590Z
Comments.Text: 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
Comments.UserDisplayName: Bioathlete
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-11T05:56:31.317Z
Comments.Text: This is crossposted on biostars: https://www.biostars.org/p/357824/
Comments.UserDisplayName: finswimmer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-15T17:52:23.350Z
Comments.Text: Do you want the reads that contain the amplicon? If you know the primer sequences you could do this pretty easily
Comments.UserDisplayName: d_kennetz
Tags: <ngs>
Title: amplicon sequencing set up
ThreadText: # 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
  
  