RNA_Seq_Reference_Based_Sequencing

Drosophila melanogaster RNA-seq Analysis Pipeline

A complete RNA-seq analysis pipeline for studying tumor-free (w1118) vs tumor-bearing (MARCM RasV12, scrib1) Drosophila larvae, from raw data download to differential expression analysis.

Dataset Information

• SRA Accession: SRP324433
• Study: RNAseq from cuticles of tumor-free and tumor-bearing Drosophila larvae
• Samples:
  • Control (w1118): SRR14850651, SRR14850663
  • Treated (MARCM RasV12, scrib1): SRR14850697, SRR14850698

Pipeline Overview

1. Data acquisition from SRA/ENA
2. Quality control with FastQC
3. Adapter trimming with fastp
4. Alignment using:
   • STAR (splice-aware)
   • HISAT2 (alternative)
5. Quantification and differential expression with Cufflinks/Cuffdiff

Requirements

Software

• SRA Toolkit (for direct SRA downloads)
• FastQC
• fastp
• STAR
• HISAT2
• samtools
• Cufflinks

Reference Data

• Drosophila melanogaster (dm6) genome:

  wget https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gz
  gunzip dm6.fa.gz