Bioinformatics Data analysis:

Comprehensive Differential Gene Expression (DEG) analysis services for high-throughput sequencing datasets, including:

RNA-seq (mRNA sequencing)

miRNA-seq

CRISPR sgRNA screen data

With 6+ years of experience in transcriptomic data analysis, I offer end-to-end analytical support — from raw FASTQ files to biological interpretation and publication-ready results.

Analysis

✔ Quality control (FastQC, MultiQC)
✔ Adapter trimming & filtering (fastp/Trimmomatic)
✔ Alignment (HISAT2/STAR) or pseudoalignment (Salmon)
✔ Read quantification (featureCounts/HTSeq)
✔ Normalization & DEG analysis (DESeq2/edgeR/limma)
✔ PCA & clustering
✔ Volcano plots & heatmaps
✔ Functional enrichment (GO/KEGG)
✔ Pathway analysis
✔ Publication-ready figures

CRISPR Screen Analysis

✔ sgRNA count normalization
✔ Identification of enriched/depleted genes (MAGeCK)
✔ Gene ranking and hit identification
✔ Pathway enrichment analysis of candidate genes
✔ Visualization of screening results

Deliverables

DEG tables (Excel + CSV format)

Statistical summary (log2FC, adjusted p-values)

High-quality figures (PNG/PDF)

Detailed Report

Comprehensive analysis of Whole Exome Sequencing (WES) data for somatic mutation detection, commonly used in cancer genomics studies to identify tumor-specific variants by comparing tumor and matched normal samples.

Analysis Workflow

✔ Raw sequencing quality assessment (FastQC, MultiQC)
✔ Adapter trimming and quality filtering (fastp / Trimmomatic)
✔ Alignment to reference genome (BWA-MEM)
✔ Sorting and indexing of BAM files
✔ Duplicate marking (Picard MarkDuplicates)
✔ Base Quality Score Recalibration (GATK BQSR)
✔ Somatic variant calling (GATK Mutect2 / Strelka2 / VarScan2)
✔ Variant filtering (FilterMutectCalls)

Variant Annotation

✔ Functional annotation (ANNOVAR / VEP)
✔ Identification of somatic SNPs and INDELs
✔ Variant classification (missense, nonsense, frameshift, splice-site)
✔ Population frequency filtering (gnomAD, 1000 Genomes)
✔ Cancer database annotation (COSMIC, ClinVar)

Downstream Analysis

✔ Identification of tumor-specific mutations
✔ Mutation burden analysis
✔ Visualization and reporting of somatic variants

Deliverables

✔ Annotated somatic variant tables (VCF + Excel format)
✔ Variant impact summaries
✔ Mutation statistics and QC reports
✔ Publication-quality figures
✔ Detailed analysis report

Pricing (depending on sample size and complexity)

RNA-seq (Standard DEG):₹15,000 – ₹30,000
miRNA-seq: ₹18,000 – ₹35,000

CRISPR sgRNA Screen:₹18,000 – ₹35,000

Whole Exome Somatic Variant Analysis: ₹25,000 – ₹45,000

***EXTRA ₹8000 Full manuscript drafting (Introduction + Methods + Results + Discussion)Exome Sequencing Data Analysis (Somatic Variant Calling)