How nehagupta-16/rnaseq-data-analysis works
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 Read alignment · rseqc.qsub Alignment QC · cufflinks.qsub Expression quantification · cuffdiff.qsub Differential expression
Components 13
Read processing
- Read alignment
tophat.qsub - Alignment QC
rseqc.qsub
Expression analysis
- Expression quantification
cufflinks.qsub - Differential expression
cuffdiff.qsub
Biological interpretation
- Gene profiles and heatmap
BIOLOGIST.R
Other components
- Researcher
- Paired-end reads
- Genome references
- Aligned BAM
- QC metrics
- FPKM tracing files
- Gene expression differences
- Plots and heatmap
Connections 18
- Researcher → Read alignment: submits job
README.md - Paired-end reads → Read alignment: provides reads
README.md - Genome references → Read alignment: provides genome
README.md - Read alignment → Aligned BAM: outputs BAM
README.md - Researcher → Alignment QC: submits job
README.md - Aligned BAM → Alignment QC: provides alignments
README.md - Genome references → Alignment QC: provides BED
README.md - Alignment QC → QC metrics: outputs metrics
README.md - Researcher → Expression quantification: submits job
README.md - Aligned BAM → Expression quantification: provides alignments
README.md - Genome references → Expression quantification: provides annotations
README.md - Expression quantification → FPKM tracing files: outputs FPKM
README.md - Researcher → Differential expression: submits job
README.md - Aligned BAM → Differential expression: provides alignments
README.md - Differential expression → Gene expression differences: outputs differences
README.md - Researcher → Gene profiles and heatmap: runs analysis
README.md - FPKM tracing files → Gene profiles and heatmap: provides expression
README.md - Gene profiles and heatmap → Plots and heatmap: reports results
README.md