Wozniak_2022

The "Wozniak_2022_VOC_Data.zip" dataset contains chromatographs of volatile organic compounds (VOC) emitted by different Capsella genotypes. VOCs were analyzed by the headspace solid phase microextraction (HS-SPME) and gas chromatography coupled with electron impact ionization/quadrupole mass spectrometry (GC-EI-MS). It also includes Supplemental Data1, which shows the average responses per individual of all mass features observed after non-targeted profiling of the volatile organic compounds. In this table, blank values for each mass fragment were substracted and the response was stadardized to the number of open flowers. 
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In the PiNPiS_scripts folder are scripts for computing PiNPiS for every gene in the genome from standard sequencing files (  Available also on github https://github.com/kevinfrsartori/Whole_Genome_PiNPiS)

<strong>Required data:</strong>
-for the genetic reference: the CDS ".cds.fa", the gff ".gene.gff3", the protein "protein.fa".<br>
-for the variants: a VCF file ".vcf".
<strong>Procedure:</strong>
Follow the 0-Steps_PiNPiS text file.
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"Wozniak_2022_VOC_Data.zip"数据集包含不同荠属（Capsella）基因型释放的挥发性有机化合物（Volatile Organic Compounds，VOC）的色谱图。该类挥发性有机化合物的分析采用顶空固相微萃取（Headspace Solid Phase Microextraction，HS-SPME）结合气相色谱-电子轰击电离/四极杆质谱（Gas Chromatography coupled with Electron Impact Ionization/Quadrupole Mass Spectrometry，GC-EI-MS）完成。该数据集还包含补充数据1，其展示了对挥发性有机化合物进行非靶向谱图分析后观测到的所有质量特征的单样本平均响应值。该表格中已扣除每个质量片段的空白值，并将响应值标准化至开放花朵数量。

PiNPiS_scripts文件夹中包含用于从标准测序文件中计算全基因组每个基因的PiNPiS值的脚本（该脚本同样可在GitHub平台https://github.com/kevinfrsartori/Whole_Genome_PiNPiS获取）。

**所需数据：**
- 遗传参考数据：编码序列（Coding Sequence，CDS）文件".cds.fa"、通用特征格式3（General Feature Format 3，GFF3）注释文件".gene.gff3"以及蛋白质序列文件"protein.fa"。
- 变异数据：变异调用格式（Variant Call Format，VCF）文件".vcf"。
**操作流程：**
请遵照0-Steps_PiNPiS文本文件执行操作。