MuskanKashyap-15/RNA-Seq-Analysis-of-Human-LCLs

An exploration of gene expression in Yoruba individuals of Nigeria using public RNA-Seq data. # 🧬 RNA-Seq Analysis of Human LCLs This project performs RNA-Seq data analysis on human lymphoblastoid cell lines (LCLs), focusing on variant detection. The pipeline includes quality control, adapter trimming, read alignment to the human reference genome (hg38), visualization using IGV, and variant calling with BCFtools. All tools used are open-source and run on Ubuntu via WSL (Windows Subsystem for Linux). --- ## 📁 Files - `SRR19762473_1.fastq`, `SRR19762473_2.fastq` — Raw paired-end FASTQ files from NCBI SRA. - `SRR19762473_1_fastqc.html`, `SRR19762473_2_fastqc.html` — FastQC reports before trimming. - `SRR19762473_trimmed_1P.fastq`, `SRR19762473_trimmed_2P.fastq` — Paired-end reads after Trimmomatic trimming. - `SRR19762473_trimmed_1U.fastq`, `SRR19762473_trimmed_2U.fastq` — Unpaired reads after trimming. - `SRR19762473_trimmed_1P_fastqc.html`, `SRR19762473_trimmed_2P_fastqc.html` — FastQC reports after trimming. - `SRR19762473_aligned.sam` — SAM file generated by BWA after alignment to hg38. - `SRR19762473_aligned_sorted.bam` — BAM file sorted by coordinate using SAMtools. - `SRR19762473_aligned_sorted.bam.bai` — BAM index file used for visualization in IGV. - `SRR19762473_variants.bcf` — Raw binary variant call file (BCF) from BCFtools. - `SRR19762473_variants.vcf` — VCF file version of the raw variants. - `SRR19762473_variants_filtered.vcf` — Final filtered variant calls (QUAL > 30, DP > 10). - `README.md` — Project documentation (this file). --- ## ⚙️ Workflow Overview ### 1. **Data Download** - Used `prefetch` and `fasterq-dump` from SRA Toolkit to retrieve FASTQ files. ### 2. **Quality Check (FastQC)** - Evaluated raw and trimmed reads for quality, overrepresented sequences, and adapter content. - An .html report for each input file (SRR19762473_1_fastqc.html) - FASTQC Report 1 - FASTQC Report 2 ### 3. **Trimming (Trimmomatic)** - Removed low-quality bases and Illumina adapters from paired-end reads. - FastQC produces - html reports for each file …