# nehagupta-16/rnaseq-data-analysis architecture

> Architecture diagram of the GitHub repository nehagupta-16/rnaseq-data-analysis, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-30). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/nehagupta-16/rnaseq-data-analysis
- Repository: https://github.com/nehagupta-16/rnaseq-data-analysis

## Overview

This repository documents a mouse cardiac-regeneration RNA-seq analysis, from paired-end reads through alignment and expression analysis to biological plots and a heatmap. The main interpretation step is BIOLOGIST.R, which takes FPKM_tracing files and reports expression profiles for selected gene groups and a clustered heatmap of top differentially expressed genes. Separate branches provide alignment quality-control metrics and differential-expression results. Relationships here are based on the README; no source excerpts were available, so implementation details beyond those documented are omitted.

Main entry points: [`tophat.qsub`](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/tophat.qsub) (Read alignment), [`rseqc.qsub`](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/rseqc.qsub) (Alignment QC), [`cufflinks.qsub`](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/cufflinks.qsub) (Expression quantification), [`cuffdiff.qsub`](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/cuffdiff.qsub) (Differential expression)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_seq["Read processing"]
  node_align["Read alignment<br/>[tophat.qsub]"]
  node_qc["Alignment QC<br/>[rseqc.qsub]"]
end

subgraph group_expr["Expression analysis"]
  node_quant["Expression quantification<br/>[cufflinks.qsub]"]
  node_diff["Differential expression<br/>[cuffdiff.qsub]"]
end

subgraph group_bio["Biological interpretation"]
  node_biology["Gene profiles and heatmap<br/>[BIOLOGIST.R]"]
end

node_researcher(("Researcher"))
node_reads["Paired-end reads"]
node_refs["Genome references"]
node_bam["Aligned BAM"]
node_qcresults["QC metrics"]
node_fpkm["FPKM tracing files"]
node_diffresults["Gene expression differences"]
node_figures["Plots and heatmap"]

node_researcher -->|"submits job"| node_align
node_reads -->|"provides reads"| node_align
node_refs -->|"provides genome"| node_align
node_align -->|"outputs BAM"| node_bam
node_researcher -->|"submits job"| node_qc
node_bam -->|"provides alignments"| node_qc
node_refs -->|"provides BED"| node_qc
node_qc -->|"outputs metrics"| node_qcresults
node_researcher -->|"submits job"| node_quant
node_bam -->|"provides alignments"| node_quant
node_refs -->|"provides annotations"| node_quant
node_quant -->|"outputs FPKM"| node_fpkm
node_researcher -->|"submits job"| node_diff
node_bam -->|"provides alignments"| node_diff
node_diff -->|"outputs differences"| node_diffresults
node_researcher -->|"runs analysis"| node_biology
node_fpkm -->|"provides expression"| node_biology
node_biology -->|"reports results"| node_figures

click node_align "https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/tophat.qsub"
click node_qc "https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/rseqc.qsub"
click node_quant "https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/cufflinks.qsub"
click node_diff "https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/cuffdiff.qsub"
click node_biology "https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/BIOLOGIST.R"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_align,node_qc toneBlue
class node_quant,node_diff toneAmber
class node_biology toneMint
class node_researcher,node_reads,node_refs,node_bam,node_qcresults,node_fpkm,node_diffresults,node_figures toneIndigo
```

## Components

### Read processing

- [Read alignment](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/tophat.qsub): `tophat.qsub`
- [Alignment QC](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/rseqc.qsub): `rseqc.qsub`

### Expression analysis

- [Expression quantification](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/cufflinks.qsub): `cufflinks.qsub`
- [Differential expression](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/cuffdiff.qsub): `cuffdiff.qsub`

### Biological interpretation

- [Gene profiles and heatmap](https://github.com/nehagupta-16/rnaseq-data-analysis/blob/main/BIOLOGIST.R): `BIOLOGIST.R`

### Other components

- **Researcher**
- **Paired-end reads**
- **Genome references**
- **Aligned BAM**
- **QC metrics**
- **FPKM tracing files**
- **Gene expression differences**
- **Plots and heatmap**

## Connections

- Researcher → Read alignment: submits job (evidence: `README.md`)
- Paired-end reads → Read alignment: provides reads (evidence: `README.md`)
- Genome references → Read alignment: provides genome (evidence: `README.md`)
- Read alignment → Aligned BAM: outputs BAM (evidence: `README.md`)
- Researcher → Alignment QC: submits job (evidence: `README.md`)
- Aligned BAM → Alignment QC: provides alignments (evidence: `README.md`)
- Genome references → Alignment QC: provides BED (evidence: `README.md`)
- Alignment QC → QC metrics: outputs metrics (evidence: `README.md`)
- Researcher → Expression quantification: submits job (evidence: `README.md`)
- Aligned BAM → Expression quantification: provides alignments (evidence: `README.md`)
- Genome references → Expression quantification: provides annotations (evidence: `README.md`)
- Expression quantification → FPKM tracing files: outputs FPKM (evidence: `README.md`)
- Researcher → Differential expression: submits job (evidence: `README.md`)
- Aligned BAM → Differential expression: provides alignments (evidence: `README.md`)
- Differential expression → Gene expression differences: outputs differences (evidence: `README.md`)
- Researcher → Gene profiles and heatmap: runs analysis (evidence: `README.md`)
- FPKM tracing files → Gene profiles and heatmap: provides expression (evidence: `README.md`)
- Gene profiles and heatmap → Plots and heatmap: reports results (evidence: `README.md`)