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RNASeq analysis preformed for the module QBio304: Applied Bioinformatics

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Name		Name	Last commit message	Last commit date
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analysis_results		analysis_results
fastqc_results		fastqc_results
kallisto		kallisto
trimmomatic		trimmomatic
.gitignore		.gitignore
1_import_filter_norm.R		1_import_filter_norm.R
2_analysis.R		2_analysis.R
README.md		README.md
RNASeq_Analysis.Rproj		RNASeq_Analysis.Rproj
checksums.txt		checksums.txt
study_design.txt		study_design.txt

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RNASeq_Analysis

RNASeq analysis preformed as part of the module QBio304: Applied Bioinformatics

R script templates taken from https://github.com/NAMlab/QBIO

Source study: https://www.researchgate.net/publication/359037824_Metabolite_Profiling_and_Transcriptome_Analysis_Revealed_the_Conserved_Transcriptional_Regulation_Mechanism_of_Caffeine_Biosynthesis_in_Tea_and_Coffee_Plants

Raw Data:
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA798825
https://www.ncbi.nlm.nih.gov/sra/SRX13836512
https://www.ncbi.nlm.nih.gov/sra/SRX13836513
https://www.ncbi.nlm.nih.gov/sra/SRX13836514
https://www.ncbi.nlm.nih.gov/sra/SRX13836515
https://www.ncbi.nlm.nih.gov/sra/SRX13836506
https://www.ncbi.nlm.nih.gov/sra/SRX13836507
https://www.ncbi.nlm.nih.gov/sra/SRX13836508
https://www.ncbi.nlm.nih.gov/sra/SRX13836509

Coffea Canephora ensembl genome: https://plants.ensembl.org/Coffea_canephora/Info/Index

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RNASeq analysis preformed for the module QBio304: Applied Bioinformatics

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