文件列表:

Diversity (0, 2022-12-09)
Diversity\JU-Reference-Concatenated.fa (13581, 2022-12-09)
Diversity\JU-Segments_Con.gtf.txt (1547, 2022-12-09)
Diversity\runSNPGenie_Diversity.sh (637, 2022-12-09)
SNPdat (0, 2022-12-09)
SNPdat\H5.gtf.txt (1517, 2022-12-09)
SNPdat\SNPdat_Parse.V3.sh (1286, 2022-12-09)
SNPdat\SNPdat_v1.0.5.pl (108485, 2022-12-09)
VariantAnalysis (0, 2022-12-09)
VariantAnalysis\1_Auto_VCFvariant_Jurre.R (1536, 2022-12-09)
VariantAnalysis\1_VCFvariant_Jurre.sh (1538, 2022-12-09)
VariantAnalysis\H5_CNS_Jurre.fa (13590, 2022-12-09)
VariantAnalysis\LoFreqAnalysis.sh (2600, 2022-12-09)
VariantAnalysis\colnameSample.R (412, 2022-12-09)

# Evolution-of-highly-pathogenic-H5N1-influenza-A-virus-in-the-central-nervous-system-of-ferrets This repository has the code used to determine presence of variants and to calculate diversity (π) in "Evolution-of-highly-pathogenic-H5N1-influenza-A-virus-in-the-central-nervous-system-of-ferrets" # Variant Analysis and evaluation of amino acid substitutions. To run variant analysis using LoFreqAnalysis.sh, fastq files (R1 and R2) need to be within the same folder as H5_CNS_Jurre.fa. PATH in .bashrc should be /Users/YOURUSERNAME/scripts/iSNV. Scripts should be located within iSNV folder. Afterwards, files present in 04_Results needs to be modified using 1_VCFvariant_Jurre.sh. The output of this step will be used by SNPdat_Parse.V3.sh. This will produce a table showing the amino acid changes produced by the variant. # Calculation of π (Diversity) For the calculation of diversity, I used the script runSNPGenie_Diversity.sh which is dependent on SNPGenie (PMID:26227143). A concatenated version of the influenza genome was used as a reference (JU-Reference-Concatenated.fa). To run the analysis, the directory should have the fastq files, fasta file and the GTF file.

近期下载者：

相关文件：

评论：[我要评论] [举报此文件]

收藏者：