Analysis of OMICS data – 2024

4×45 minutes practicals for 13 weeks

Lecturers: Ari Eszter (arieszter@gmail.com), Dávid Jónás (jonas.david.gen@hotmail.com), Gitta Schlosser (gitta.schlosser@gmail.com), Ágoston Hunya (ago.hunya@gmail.com)

Name of the MS Teams group: Crs 23-24-2 anomicib22lm GEN Omika adatok elemzése GY

The platforms of the practicals

• in person: ELTE TTK South Building floor 7 room 7-424
• from 12:30 to 15:45 on Thursdays

Requirements

• The requirements of the practical are available here: Requirements of OMICS practicals
• Attendance sheet OMICS

Technical issues

Terminal software to install that ables X11 forwarding when logging in to the Linux server:

• Windows: MobaXterm home edition, portable version.
• Mac (if needed, since theoretically the Terminal also works so try this native software first, see below): XQuartz.
• Linux (and Mac): just type ssh -p 2227 -X USERNAME@rstudio.dlab.elte.hu where the -X argument allows the X11 forwarding.

Schedule

1. Introduction to the environment and to bash

ssh, basic bash (Linux) commands, handling big data

Applied software: terminal, text editor (vim, emacs, gedit, etc.; I will teach a bit about vim)

Lecture slides, Practical tasks

15 Feb, Dávid Jónás

2. Introduction to next-generation sequencing (NGS)
   Overview of main types of high-throughput DNA sequencing technologies: Illumina, IonTorrent, Oxford Nanopore, PacBio. Different sequencing solutions: multiplex sequencing and barcoding, single-end – paired-end sequencing. Introduction to the usage of the offline genome browser: IGV Viewer. 

Applied software: IGV Viewer
Lecture slides: 02 L Introduction to next generation sequencing

Practical tasks (download and open the local version in a browser)

useful material: Sequencing Buyers Guide-2022

22 Feb, Eszter Ari

3. Genomics part 1
   Overview of NGS-related data and file types: fastQ, SAM, BAM, BED, GFF, GTF, etc. Downloading genome sequence and annotation files. Practising bash commands to open files, search patterns, pipe commands, etc.

Applied software: bedops, vcftools, bedtools, samtools, bamtools

Lecture slides, Practical tasks

29 Feb, Dávid Jónás

4. Genomics part 2
   Genome re-sequencing: quality filtering, read-mapping, variant analysis.

Applied software: sratoolkit, FastQC, BWA, samtools, bamtools, picard

Lecture slides, Practical tasks

7 March, Dávid Jónás

5. Genomics part 3

Sequence repositories and additional scripting.

Applied software: sratoolkit, FastQC, BWA, hisat2, samtools, bamtools, picard

Lecture slides, Practical tasks

14 March, Dávid Jónás

6. Chip-seq analysis

Mapping, peak calling, defining binding regions, differential peak calling.

Applied software: FastQC, Bowtie2, samtools, bamtools, bedtools, MACS2, Homer, R, AWK

Lecture slides, Practical tasks

21 March, Dávid Jónás

Spring break

7. Marker gene amplification metagenomics

Data analysis of 16S rRNA sequencing of a microbiome, OTU picking, taxonomic assignment, and calculating diversities.

Applied software: R, Rstudio, packages: dada, phyloseq, Biostrings, ggplot2

Applied R packages: dada2, phyloseq, Biostrings, ggplot2

Lecture slides, Practical tasks
4 April, Ágoston Hunya

8. Transcriptomics part 1

Introduction to transcriptomics, RNA-seq quality filtering, read-mapping, and read-counting.

Applied software: RStudio server

Applied R packages: ShortRead, Rsubread, Rsamtools

Lecture slides, Practical tasks

11 April, Eszter Ari

9. Transcriptomics part 2

RNA-seq data analysis, differential expression analysis.

Applied software: RStudio

Applied R packages: pheatmap, stats, ggplot2, ggfortify, DESeq2, EDASeq
Lecture slides, Practical tasks

18 April, Eszter Ari

10. Functional enrichment analysis

Functional enrichment analysis of differentially expressed genes, using Gene Ontology (GO) and pathway databases.

Applied software: Rstudio pro

Applied R packages: clusterProfiler, org.Hs.eg.db, tidyr, dplyr, and enrichplot

Lecture slides: 10 L Functional enrichment analysis, Practical tasks

25 April, Eszter Ari

11. Proteomics
    Applied software: MassLynx, ProteinLynx, Mascot, Protein Prospector
    Practical tasks
    2 May, Gitta Schlosser
12. Preparation of the exam material –-- Eötvös Day
    consultation
    9 May, Eszter Ari, Dávid Jónás, Ágoston Hunya
13. Presentation of the results

Students present the results of their analysis.

16 May, Eszter Ari, Dávid Jónás