ecSeq Bioinformatics Course

ecSeq Bioinformatics Course

4-day workshop on Linux, Next Generation Sequencing and RNA sequencing and Data Analysis.


2.04 to 5.04.19


BMC, PC room N02.008 - Limited space: early registration recommended!


1. Linux for Bioinformatics

• Introduction to the command line and important commands
• Combining commands by piping and redirection
• Introduction to bioinformatics file formats (e.g. FASTA, BED) and databases (e.g. UCSC)

2. Introduction to NGS data analysis

• Introduction to sequencing technologies from a data analysts view
• Raw sequence files (FASTQ format)
• Preprocessing of raw reads: quality control (FastQC), adapter clipping, quality trimming
• Introduction to read mapping (Alignment methods, Mapping heuristics)
• Read mapping (BWA, BWA-MEM, Bowtie2, STAR, segemehl)
• Mapping output (SAM/BAM format)
• Mapping statistics
• Visualization of mapped reads (IGV, UCSC)

3. RNA-seq Data Analyses

• Understand split-read mapping
• Run different split-read mappers (tophat, segemehl, STAR)
• Understand the Tuxedo Suite (cufflinks, cuffcompare, cuffmerge, cuffdiff, etc.)
• Predict new transcripts/isoforms using cufflinks/cuffmerge
• Quantify exons/genes/transcripts
• Predict Differential exon usage using DEXseq, differential gene expression using DEseq and differential isoform expression using cuffdiff

The course fee will be covered for IMPRS-TP students.

Please contact the IMPRS-TP coordination office, if you are interested in joining the course!

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