Answers.Body: <p>At the  NCBI you can find <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_024036415.1/" rel="nofollow noreferrer">Prochilodus magdalenae genome assembly</a> and one <a href="https://www.ncbi.nlm.nih.gov/sra/?term=txid27695%5BOrganism:noexp%5D" rel="nofollow noreferrer">P.lineatus WGS SRA dataset</a>. That means:</p>
  <ul>
  <li>you have a genomic assembly  of the hopefully closely related species from the same genus and construct a genomic database to map your FASTQ reads</li>
  <li>you may roughly estimate how much difference is between the two Prochilodus species by mapping SRX8237586 FASTQ</li>
  </ul>
  <p>No idea how the GBS multiplexing was done, but to make any sense you must be able to either split the FASTQ into the individual FASTQ files specific to samples or have the sample ID somehow encoded in the read names. Then you map FASTQs to the <strong>Prochilodus magdalenae genome</strong> using <a href="https://github.com/bwa-mem2/bwa-mem2" rel="nofollow noreferrer">bwa-mem2</a> on the Linux server / cluster or in the worst case scenario Linux workstation with as much RAM and CPU cores as possible.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-05-14T11:58:26.593Z
Answers.LastActivityDate: 2024-05-14T11:58:26.593Z
Answers.UserDisplayName: darked89
Body: <p>I have a GBS sequence on the Illumina platform that in the FASTQC quality report has “Failure” in : Per tile sequence quality, Per base sequence content, Sequence Duplication Levels and Adapter Content. I don't have much experience with bioinformatics and I'm not sure what I should do.</p>
  <p>Note: The sequencing was of 119 samples, where 80 of these were of Prochilodus lineatus, 30 of Leporinus fasciatus and 9 samples of Piaractus mesopotamicus. These samples were sequenced together but my work involves analyzing only Prochilodus lineatus.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-13T23:30:58.087Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-14T12:01:00.567Z
Comments.Text: If you are really new to this the best is to find some local(?) bioinformatician and collaborate. He/she should be able to walk you through all the steps.
Comments.UserDisplayName: darked89
Tags: <ngs><genome><snp><fastqc>
Title: GBS- 'Failure' in, Per base sequence content, Sequence Duplication Levels, and Adapter Content
ThreadText: # GBS- 'Failure' in, Per base sequence content, Sequence Duplication Levels, and Adapter Content
  
  (Asked by: username_0 on 2024-05-13)
  
  I have a GBS sequence on the Illumina platform that in the FASTQC quality report has “Failure” in : Per tile sequence quality, Per base sequence content, Sequence Duplication Levels and Adapter Content. I don't have much experience with bioinformatics and I'm not sure what I should do.
  
  Note: The sequencing was of 119 samples, where 80 of these were of Prochilodus lineatus, 30 of Leporinus fasciatus and 9 samples of Piaractus mesopotamicus. These samples were sequenced together but my work involves analyzing only Prochilodus lineatus.
  
  **Tags:** ngs, genome, snp, fastqc
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: If you are really new to this the best is to find some local(?) bioinformatician and collaborate. He/she should be able to walk you through all the steps.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-05-14. Score: 0
  
  At the NCBI you can find [Prochilodus magdalenae genome assembly](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_024036415.1/) and one [P.lineatus WGS SRA dataset](https://www.ncbi.nlm.nih.gov/sra/?term=txid27695%5BOrganism:noexp%5D). That means:
  
  * you have a genomic assembly of the hopefully closely related species from the same genus and construct a genomic database to map your FASTQ reads
  * you may roughly estimate how much difference is between the two Prochilodus species by mapping SRX8237586 FASTQ
  
  No idea how the GBS multiplexing was done, but to make any sense you must be able to either split the FASTQ into the individual FASTQ files specific to samples or have the sample ID somehow encoded in the read names. Then you map FASTQs to the **Prochilodus magdalenae genome** using [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) on the Linux server / cluster or in the worst case scenario Linux workstation with as much RAM and CPU cores as possible.
  
  
  ---
  
  