ShawnWx2019/P.sibiricum_code

Analysis code for P.sibiricum paper

Analysis and visualize code of P.sibiricum research.

Citation

Ou X^#*., Wang X^#., Zhao B., Zhao Y., Liu HQ., Chang Y., Wang Z., Yang W., Zhang X^*., Yu K^*. Metabolome and transcriptome signatures shed light on the anti-obesity effect of Polygonatum sibiricum. 2023, Frontiers in Plant Science., 14:1273.

Metabolomics data analysis

Metabolomics data was processed using R packages: TidyMass.

From peak picking to metabolite annotation was completed using the HPC-TidyMass pipeline , in which only the peak picking step was utilized.

## The help information of Tidymass pipeline
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/home/data/shawn/01.src/02.script/02.Tidymass/runTidymass.sh: option requires an argument -- h
Tidymass pipeline part1. Date transform ,peak picking and annotation
Usage:
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runTidymass [-i input] [-t type] [-c column]
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Author Shawn Wang (shawnwang2016@126.com)
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Date Tus Feb 09, 2023
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Version V.0.0.0.99 beta
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Description
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[-i]:input,   The file path of .raw data
[-t]:type,  The type of ion model, 1: NEG+POS in one file, 2: NEG and POS in differnet files
[-c]:column,  rp or hilic
###############################################################################################

bash runTidymass.sh -i raw/p_sibiricum -t 1 -c rp

Content

Step1. convert .raw data to .mzXML and .mgf

• .raw 2 .mzXML: 01.msconvert.sh

• .raw 2 .mgf: 03.ms2convert.sh

Step2. Data cleaning and normalization

• Raw data overview: OverviewMetabolomicsData.R

• Data cleaning and normalization: DataCleaning.R

• Data annotation: DataAnnotation.R

• Remove redundancy and classification: RemoveRedundancyandClassification.R

• Metabolomics Mfuzz: MetaMfuzz.R

Step3. Pacbio visualization

• Transcript annotation integration: PacbioVisualization.R

• Picbio BUSCO analysis: BUSCO.R

Step4. NGS data analysis

• DEG analysis and visualization, (hclust, 3D pca, DEG, mFuzz): DEG_analysis.R

• PSP pathway: PSP.R

• unFA pathway: unFA.R

• phloretin pathway: phloretin.R