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hbv_primer_fidelity

Use "HBV_oligo_genotype_selection" instead

https://github.com/tgrudda1/hbv_primer_fidelity

Science Score: 67.0%

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    Links to: ncbi.nlm.nih.gov
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Repository

Use "HBV_oligo_genotype_selection" instead

Basic Info
  • Host: GitHub
  • Owner: tgrudda1
  • Language: Shell
  • Default Branch: main
  • Homepage:
  • Size: 17.6 KB
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  • Watchers: 1
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  • Releases: 1
Created about 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme Citation

README.md

##Use https://github.com/tgrudda1/HBVoligogenotype_selection instead.

HBVprimerfidelity

Introduction

This is a rudimentary code to blast your HBV primers against 4,000+ full length HBV sequences, genotypes A-I, testing for pangenotypicity. Sequences are pulled from http://hvdr.bioinf.wits.ac.za/alignments/. Please cite Bell et al. (DOI: 10.1186/s40064-016-3312-0) if using this for publication. I don't really know how to code, but if this was helpful for your project please cite the work attached to this code.

Requirements

NCBI BLAST for UNIX (this was in Linux Ubuntu): https://www.ncbi.nlm.nih.gov/books/NBK52640/

RStudio: https://www.rstudio.com/products/rstudio/download/#download Within R, you'll just need 'tidyverse' for this: install.packages('tidyverse')

Process

Make a new folder for your - PrimerBlast.sh - Primers.fa (be sure your primers are labelled and in FASTA format)

In your terminal, navigate to your new folder and run the shell

sh PrimerBlast.sh

This will align your primers to each genotype and export these to a .txt file.

Your done with the command line now and can move to RStudio.

Set your working directory to the original file you created which also contains your new genotype-specific alignments. Open the "Primer Alignments.Rmd" notebook and run the chunk by hitting the "play" button at the top right of the highlighted chunk.

Output

In the "a2i.match" dataframe, columns are the following: - primer - GENOTYPE - gen.len -the number of full length sequences you blasted against - perf.count -the number of sequences your primer aligned to with zero mismatches - offby1.count -the number of sequences your primer aligned to with up to 1 mismatch - perf.perc -the percentage of sequences your primer aligned to with zero mismatches - offby1.perc -the percentage of sequnces your primer aligned to with up to 1 mismatch

This is the relevant data you need to check how pangenotypic your primer sets will be. Once you're in R you can play around with visual representations of your data, but this is all you need to get started.

Owner

  • Login: tgrudda1
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this code, please cite it as below."
authors:
  - family-names: Grudda
    given-names: Tanner
    orcid: https://orcid.org/0000-0001-9045-2753
title: "HBV_primer_fidelity"
version: 1.0
doi: 10.5281/zenodo.6342294
date-released: 2022-02-21

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