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# System prepended metadata

title: Bioinformatics Core Facility services

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# Bioinformatics Core Facility services

[***Acknowledgement***](https://eu.ilabsolutions.com/service_center/show_external/3672)

All users must acknowledge the Core Facility in publications that include data generated at the Core Facility.

What to always include:

“We acknowledge the Core Facility at the Faculty of Medicine and Health Sciences, Linköping University for providing assistance in [technology...].”

Significant help from a specific researcher at the Core Facility and acknowledgement by name:

“The authors thank Dr [name] at the Core Facility at the Faculty of Medicine and Health Sciences, Linköping University for [support and guidance in…].”

Substantial contributions that merit co-authorship of papers

If scientists from the Core Facility contribute more than routine techniques and when they make a substantial intellectual and/or experimental contribution to a research study, they should be co-authors of papers that use these data. These applies to: (1) Intellectual contribution, concept, design of project, critical input, and original ideas: (2) **Data analysis and interpretation, preparation of figures and tables for publications;** (3) Write a portion of the paper, draft the article, or revise it critically for intellectual content. Authorship is preferably established at the beginning of the project so that both the user e.g. the PI and the Core Facility researcher are aware of each other’s criteria.

Charging for services does not preclude acknowledgement for support or co-authorship

iLab
Service Projects
- Clinical Genomics 
    - Molecular Biology
    
    - Bioinformatics
    1. DNA sequencing
        1.1. Basic analysis
        1.2. Customized analysis
     
    2. RNA sequencing
        2.1. Basic analysis
        2.2. Customized analysis
    
    3. Transcriptomic analysis
    4. Microarray analysis
    5. DNA Methylation arrays
    6. DNA Methylation Sequencing
    

## Types of Analysis
- [ ] **A. Gene Expression Analysis (Transcriptome)**

- [ ] **1. module 1**: 400 kr
1. Quality control
2. Normalization
3. Variability analysis
4. Exploratory data analysis: unsupervised clustering & Dimension reduction
5. Identification of differentially expressed genes

- [ ] **2. module 2**: 300 kr per-comparison
1. Functional enrichment analysis using gene ontology
2. Pathway enrichment analysis using 
- [ ] Reactome or
- [ ] Panther or
- [ ] KEGG

- [ ] **3. module 3**: 300 kr per-comparison
1. Network-based analysis using string
<br>

- [ ] **B. Single-Cell RNAseq Analysis**
- [ ] **1. module 1**: 1.000 kr
1. Pre-processing
2. Alignment
3. Quality control
4. Batch effect correction
5. Unsuprevised clustering
6. Cell type annotation
7. Differential expression analysis

- [ ] **2. module 2**: same as A.2. 
- [ ] **3. module 3**: same as A.3.
<br>

- [ ] **C. Microarray data analysis** 400 kr
- [ ] **1. module 1, 2, 3**: combination of A.1, A.2 and A.3
<br>

- [ ] **D. DNA Methylation** 400 kr
- [ ] **1. module 1, 2, 3**: same modules as B.1, B.2 & B.3
<br>

- [ ] **E. Exome Sequencing Analysis**
- [ ] **1. module 1**: 400 kr
1. Quality control
2. Reads alignment
3. Marking duplicates and GATK best practices
4. Variant Calling

- [ ] **2. module 2**: 400 kr
1. Variant filtering

- [ ] **3. module 3**: 300 kr
1. Annotation (VEP)

- [ ] **4. module 4**: same as A.2.
<br>

*NOTE: There will be different charges for Illumina arrays and RRBS sequencing as well as nanopore sequencing data.*
