isinaltinkaya / adv_binf_2021_week1

Teaching material used in the "Advanced Bioinformatics for Next-Generation Sequencing" class, University of Copenhagen, 2021

Advanced Bioinformatics for Next-Generation Sequencing 2021: Week 1

Day	Time	Subject	Lecturer
Day 1 - Monday	9:15 - 12	NGS data - Workflow, formats and programs	Thorfinn Sand Korneliussen, Exercises: Isin Altinkaya
Day 2 - Tuesday	13:15 - 16	Mapping - Suffix arrays and Burrows-Wheeler Transform	Rasmus A. Henriksen
Day 3 - Friday	9:15 - 12	MapQ and Genotype Likelihoods	Lei Zhao

Friday(10/9/2021, Lei Zhao): Given that the BWT algorithm is introduced, I will introduce the MapQ score, a measurement to assess alignment. Based on the On the accuracy of short read mapping. Once the short reads fragments have been mapped, different read bases will be piled up at the each genome positions. But even the read bases at the same genome position can vary a lot due to uncertainty introduced by different error schemes. I will introduce an important concept, genotype likelihood, which helps to integrate the uncertainty into the further genomic inferences. For reference, please have a read at The genome analysis toolkit: a map reduce framework for analyzing next-generation dna sequencing data, Patterns of damage in genomic DNA sequences from a Neandertal and ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data.

Getting started

Connecting to the server via SSH

X11 forwarding method will allow you to start a graphical application on the remote system and forward this application's windows to your local system. We need to enable X11 forwarding to view the plots we will be generating for the exercises.

We use -X option to enable X11 forwarding over SSH:

$ ssh -X <your_username>@<server_name_or_ip>

Replace with your remote server username. For example:

$ ssh -X [e-mail]

Setting up the working environment

If you are working on the ricco server, and therefore will not be not clonning the repository, all commands in the following seven exercises will be relative to the base directory called /TEACHING/BIOINF21/adv_binf_2021_week1

day1
├── data
│   ├── alignment
│   ├── fasta
│   ├── fastq
│   ├── reference_fasta
│   └── reference_fasta_hs37d5
├── exercises
│   ├── alignment_formats
│   ├── mapdamage
│   ├── trimming
│   └── variant_call_format
├── Makefile
└── README.md

Git is a version-control system software for tracking changes in a set of files, and is useful for coordinating work among multiple people working in collaboration. GitHub is one of the most popular git repository hosting services. Git is not covered within the scope of this class, and will only be used for downloading the exercise materials. To learn more about git and GitHub, see GithHub Lab (optional).

$ git clone https://github.com/isinaltinkaya/adv_binf_2021_week1
$ cd adv_binf_2021_week1/day1
# gunzip files
$ make unzip
# copy reference files
$ make copy