Bioinformatics Analysis Services
BIOINFORMATICS ANALYSIS SERVICE CATALOG
1. RNA-seq/miRNA/tRNA Analysis Services
| Package Code | Analysis Name | Scope | Outputs |
|---|
| 1.1 |
Basic RNA-seq QC & Alignment |
- FastQC + MultiQCA
- dapter trimming
- Reference genome alignment
- Mapping & duplication statistics
- Gene/transcript count matrix
|
- MultiQC reports (HTML file)
- BAM/CRAM files
- Raw counts tables (TSV file)
- Mapping summary statistics (TSV file)
|
| 1.2 |
Differential Expression (DE) Analysis |
- Normalization
- Batch effect correction
- DE analysis
- Volcano, MA, PCA, heatmap
|
- DE gene list (log2FC / p-adj) (TSV file)
- All figures (PDF/PNG files)
|
| 1.3.1 |
Target Gene Analysis (miRNA, tRNA) |
- TarBase / TargetScan / miRDB target analysis
|
- Target gene lists (TSV file)
|
| 1.3.2 |
Functional Enrichment Analysis |
- GO (BP/MF/CC)
- KEGG pathway
- GSEA analysis
|
- GO/KEGG tables
- All figures (dot/bar plots) (PDF/PNG files)
|
2. 16S/18S rRNA Metagenomic Analysis
| Package Code | Analysis Name | Scope | Outputs |
|---|
| 2.1 |
Taxonomic Profile & Community Structure |
- Raw data QCPrimer trimming
- ASV extraction
- Taxonomic classification
- Phylogenetic placement
- Diversity analysis (Alpha/Beta diversity)
- PCoA / Beta-diversity
|
- ASV tables (absolute + relative abundance) (TSV files)
- Taxonomy tables (TSV files)
- Interactive barplot (HTML files)
- Alpha rarefaction plots (PNG/PDF files)
- PCoA/ordination plots (PDF/PNG files)
- Diversity report (HTML files)
|
| 2.2 |
Differential Abundance Analysis |
- DA analysis (determination of taxon changes between groups)
- Statistical comparisons at taxon level
|
- Differential abundance tables (TSV files)
- All figures (PDF/PNG files)
|
| 2.3 |
Functional Potential Analysis |
- Functional prediction
- EC, KO and MetaCyc pathway predictions
- Metabolic pathway projection
|
- Functional profile tables (EC, KO, MetaCyc) (TSV files)
- Functional abundance plots (PDF/PNG files)
|
3. ATAC-seq Analysis Services
| Package Code | Analysis Name | Scope | Outputs |
|---|
| 3.1 |
QC, Alignment & Peak Calling |
- FastQC + MultiQC QC analysis
- Adapter trimming
- Alignment
- Duplicate marking & filtering
- Coverage QC
- bigWig normalization
- Peak calling
- Peak annotation
|
- FastQC & MultiQC reports
- Aligned BAM + index
- Insert size & duplication statistics
- Normalized bigWig files
- Peak lists (narrowPeak / broad
- Peak)Peak annotation tables
- FRiP scores & peak QC metrics
|
| 3.2 |
Consensus Peak Set & Differential Accessibility |
- Cross-sample peak merging
- Peak read counting
- DA analysis
- PCA & sample similarity analysis
- Volcano & heatmap generation
|
- Consensus peak matrix (raw counts TSV file)
- DA peak tables (log2FC, p-adj)
- PCA plot, sample distance heatmap, peak intersection figures (PDF/PNG files)
|
| 3.3 |
TF Activity & Motif Analysis |
|
- Motif enrichment tables (TSV files)
- IGV session (XML file)
|
4. ChIP-seq Analysis Services
| Package Code | Analysis Name | Scope | Outputs |
|---|
| 4.1 |
QC, Trimming, Alignment & Peak Calling |
- Raw data QC (FastQC, MultiQC)
- Adapter trimming
- MappingDuplicate marking & filtering
- ChIP-seq QC metrics
- Coverage QC
- Normalized bigWig creation
- Peak calling
- Peak quality metrics (FRiP, peak counts)
|
- QC reports
- Aligned BAM/CRAM + index files
- NSC/RSC scores
- Fingerprint/profile plots
- Normalized bigWig files
- Per-sample peak lists
- FRiP scores and peak QC metrics
|
| 4.2 |
Peak Annotation & Motif Analysis |
- Align peaks with genes/promoters/functional elements
- Motif enrichment analysis
- Peak-to-gene annotation QC
|
- Annotation tables (TSV files)
- Motif enrichment reports
- Peak-to-gene distribution plots (PDF/PNG files)
|
| 4.3 |
Consensus Peak Set & Differential Binding Analysis |
- Peak read counting
- Differential binding analysis
- PCA & sample similarity analysis
- Volcano / heatmap
- UpSetR intersection analysis
- IGV session file generation
|
- Consensus peak matrix (raw counts, TSV files)
- Differential peak tables (log2FC, p-adj)
- PCA plot, sample similarity heatmap (PDF/PNG files)
- UpSetR peak intersection visualizationsigv_session.xml
|
5. Single-Cell RNA-seq Analysis
| Package Code | Analysis Name | Scope | Outputs |
|---|
| 5.1 |
Basic scRNA-seq Processing |
- Cell and gene filtering (QC)
- Doublet detection (optional)
- Normalization & scaling
- Batch correction
- Dimensionality reduction (PCA)
- UMAP / t-SNE visualization
- Clustering
|
- Seurat/Scanpy object file
- QC summary report
- UMAP / t-SNE cluster visualizations (PDF/PNG files)
|
| 5.2 |
Cell Type Annotation |
- Cluster-based marker gene analysis
- Reference-based annotation (SingleR / Azimuth, etc.)
|
- Cell type annotation table (TSV files)
- Marker gene lists per cluster (TSV files)
- Marker/heatmap visualizations (PDF/PNG files)
|
| 5.3 |
Differential Expression, Trajectory & Enrichment |
- Cluster-based differential expression (DE) analysis
- Trajectory / pseudotime analysis (if applicable)
- Functional enrichment (GO / KEGG, pathway analysis)
|
- DE gene tables (TSV files)
- Trajectory / pseudotime visualizations (PDF/PNG files)
- GO/KEGG enrichment and pathway reports (TSV files)
|
6. Whole Genome Sequencing (WGS)
| Package Code | Analysis Name | Scope | Outputs |
|---|
| 6.1 |
Basic Alignment & QC |
- Raw FASTQ quality control
- Alignment to GRCh38 or desired reference
- Sort + duplicate marking
|
- BAM/CRAM + index
- MultiQC + alignment QC report
- Coverage/Depth statistics (TSV files)
|
| 6.2 |
Variant Calling (SNV + Indel) |
- Base Quality Score Recalibration (BQSR)
- Variant calling with GATK HaplotypeCaller or Deep Variant
- Variant filtering (hard-filtering or VQSR)
- Annotation: ClinVar, gnomAD, dbSNP, SnpEff / VEP
|
- VCF / VCF.gz + index
- Annotated VCF
|
| 6.3 |
Extended WGS (SV + CNV + Archiving) |
- Structural variant (SV) analysis
- CNV analysis
- Scope analysis
- Final CRAM generation
|
- SV/CNV tables and BED files
- WGS QC report (coverage, duplication, insert size etc.)
- Compressed CRAM archive file
|
7. Additional Services
| Service Code | Service | Description |
|---|
| 7.1 |
Publication Support |
Generation of additional figures and tables for packages, preparation of supplementary materials, and method writing |
| 7.2 |
Reporting |
Detailed technical report, presentation |
| 7.3 |
Pipeline Delivery |
Nextflow workflow & documentation |
| 7.4 |
Consultation |
Experiment design, data interpretation, 1:1 meeting |
8. Pricing
| Category | Package | Suggested Price (TL) |
|---|
| 1. RNA-seq / miRNA / tRNA |
1.1 QC + Alignment |
1500 TL / sample |
| 1.2 DE Analysis |
2000 TL / comparison |
| 1.3 Target Gene Analysis |
2000 TL / analysis |
| 1.3.2 GO / KEGG / GSEA |
2000 TL / comparison |
| 2. Microbiome 16S/18S |
2.1 QC + Taxonomy + Diversity |
1000 TL / sample |
| 2.2 Differential Abundance |
2000 TL / comparison |
| 2.3 Functional Profile |
2000 TL / analysis |
| 3. ATAC-seq |
3.1 QC + Peak Calling |
1500 TL / sample |
| 3.2 DA Analysis |
2000 TL / comparison |
| 3.3 Motif Analysis |
1500 TL / analysis |
| 4. ChIP-seq |
4.1 QC + Peak Calling |
1500 TL / sample |
| 4.2 Peak Annotation + Motif |
1500 TL / analysis |
| 4.3 Differential Binding |
2000 TL / comparison |
| 5. Single-cell RNA-seq |
5.1 QC + Clustering |
2000 TL / sample |
| 5.2 Cell Type Annotation |
2000 TL / sample |
| 5.3 DE + Trajectory |
3000 TL / sample |
| 6. WGS (30X) |
6.1 Alignment + QC |
2000 TL / sample |
| 6.2 SNV/Indel + Annotation |
2000 TL / sample |
| 6.3 SV + CNV |
2000 TL / sample |
| Standard Packages |
| RNA-seq Standard Package |
(QC + alignment + DE + enrichment) |
19,000 TL / 10 samples |
| Microbiome Standard Package |
(ASV + taxonomy + diversity + DA) |
12,000 TL / 10 samples |
| ATAC-seq Standard Package |
(QC + peak + motif) |
18,500 TL / 10 samples |
| ChIP-seq Standard Package |
(QC + DB + motif) |
19,000 TL / 10 samples |
| WGS Standard Package |
(QC + alignment + VC + annotation) |
18,000 TL / 10 samples |
| scRNA-seq Standard Package |
(QC + clustering + DE + annotation) |
19,000 TL / 10 samples |
| 7. Additional Services |
Publication Support |
15,000–30,000 TL |
| Technical Report |
15,000 TL |
| Nextflow Pipeline Delivery |
50,000–200,000 TL |
| Consultation (1:1, 1 hour) |
6000 TL |
IBG Bioinformatics Analysis Services provides end-to-end analytical solutions for your genomic, transcriptomic, and proteomic datasets. Our expert team manages every stage of the workflow with scientific rigor, from data preprocessing and quality control to advanced statistical analysis and interpretation.
By designing project-specific bioinformatics strategies, we aim to accelerate your research outcomes and deliver highly reliable results.
- Standard packages apply to analyses involving 10 samples or fewer; projects with larger sample sizes will be quoted separately.
- All listed prices are exclusive of VAT.
Unit Coordinator: Leman Binokay
