RNAseq data visualization of DEG's

This repository is a walkthrough on how to:

Perform RNA-seq analyses:

RNAseq_analysis.md ~Merge Illumina lane reads illumina_fastq_lane_merging.sh
~ Trimming raw fastq reads
~ Map reads to a reference genome
~ Quantify transcripts with multiBamCov
~ Perform DESeq2 analysis with Salmon output

Visualize the data:

~ Install ggvolc and its dependencies ggvolc_installation.md
~ Uploading DESeq2 data data_upload.md
~ Generating volcano plots making_figures.md

Citation information

List of packages, versions used, citations, and relevant links

ggvolc v0.1.0
https://github.com/loukesio/ggvolc

TrimGalore v0.6.7
https://github.com/FelixKrueger/TrimGalore
https://www.bioinformatics.babraham.ac.uk/index.html
doi.org/10.5281/zenodo.7598955

samtools v3.3.2
https://github.com/samtools/
https://www.htslib.org/
Li, H. et al. The Sequence Alignment/Map format and samtools. Bioinformatics. 2009; (25)2078.
doi:10.1093/bioinformatics/btp352

Salmon v0.12.0
https://github.com/COMBINE-lab/salmon
https://combine-lab.github.io/salmon/
Patro R. et al. Salmon provides fast and bias-aware quantification of transcript expression. Nature Methodss. 2021; (14)4.  doi.org/10.1038/nmeth.4197

DESeq2 v3.1.7
https://github.com/thelovelab/DESeq2
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Love MI. et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. 2014; (15)550.
doi:10.1186/s13059-014-0550-8