BulkRNAsuite

An imagination of a start-to-finish suite for Bulk RNAseq analysis that

• starts with user-submitted FASTQ files (uploaded by the user)
• checks the consistency of filenames
  • finds and merges multiplexed files, if applicable (_001, _002, _003, _004)
  • finds and treats together R1 and R2 files, if applicable
• runs Fastqc
• runs bbduk.sh to trim adapters
• runs Fastqc again on the trimmed files
• aligns the trimmed files with Salmon using GRCm39 or GRCh38 genome full indices with decoys (SAF)

Reporting

• QC results before trimming
• QC results after trimming
• TPM matrix
• DEGs for each pairwise comparison in the list of all available groups
• PCA
• Interactive (plotly-based) Volcano plots for each pairwise comparison in the list of all available groups
• Enriched terms based on the DEGs for each pairwise comparison in the list of all available groups
• Dorothea TF regulon enrichment for each pairwise DEGs
• GSVA analysis