Veranstaltungsart:Vorlesung/Praktikum
Zugeordnete Person: Manja Marz
Termin: Do, 08:00 – 10:00 Uhr
Current material can be found in Moodle.
Lecture Slides from previous semesters:
Original Literatur: (pdfs for download)
- A Comparison of Annotation in Two Bos Taurus Assemblies (55-60% of two bos taurus assemblies identical)
- Multi-Platform Next-Generation Sequencing of the Domestic Turkey (From Cells to Multiple Fasta files)
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- How to apply de Bruijn graphs to genome assembly
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (Bowtie)
- Fast gapped-read alignment with Bowtie 2
- Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures (segemehl)
- Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
- The primary transcriptome of the major human pathogen Helicobacter pylori
- Traces of post-transcriptional RNA modifications in deep sequencing data
- Comprehensive comparative analysis of strand-specific RNA sequencing methods
Lehrmaterial:
- Workflow 454 sequencing
- Workflow Illumina sequencing
- Workflow SOLiD sequencing and calculation
- Performance SOLiD sequencing (pg 10)
- Chromatogram
- Next-generation sequencing technologies (Sanger|Pyro|IonTorrent|SOLiD|Illumina|SMRT PacBio|Nanopore|FASTQ+Phred)
- Quantification and Normalization
- script for FPKM, TPM, …
Links:
Media:
- Illumina animation youtube
- PacBio animation youtube 1 | youtube 2
- Ion Torrent sequencing animation
- 10x animation youtube 1 | youtube 2
- Nanopore sequencing animation
- History of single cell sequencing
- Cufflinks developer Dr. Lior Pachter talking about RNA-Seq relative abundances and why to use TPM and not FPKM