# INF-BIOX121 H14

## High Throughput Sequencing technologies and bioinformatics analysis

This is the wiki for the fall 2014 edition of the credited courses INF-BIO9121 and INF-BIO5121 offered by the Department of Informatics and the Department of Biosciences at the University of Oslo (UiO). Students taking the course for credit should register through StudentWeb. NOTE registration is now closed and you should have been notified if you have been offered a place for credit.

Participants not taking the course for credits should have registered before August 28. NOTE registration is now closed. Feedback on participation will be given on or soon after September 5th. (Soon to be) active users of the organising platforms will be given priority.

The High Throughput Sequencing technologies and bioinformatics analysis course consists of three weeks, four days each week, of lectures and practicals, and a final take-home exam (one week), plus reading material.

Both INF-BIO5121 (M.Sc. level) and INF-BIO9121 (Ph.D. level) are 10 study point courses.

## Time and place

The course will be offered in weeks 41, 42 and 43, autumn 2014, i.e. October 6 - 24. Each day, Monday - Thursday, will consist of lectures and (mainly) exercises/practical labs between 09:00 and 17:00. Lunch will usually be between 12:00 and 13:00. You will have to bring your own lunch or buy lunch in the local cantina. NOTE Fridays off!

Lecture room: All lectures/exercises will be given in lecture room Cobol (room 3452) in Ole-Johan Dahls hus (IFI2). A map showing the location of the building is found here. The building is located next to the Forskningsparken metro and tram stations.

## Course description

This three week, intensive course will provide knowledge of high throughput sequencing technologies and hands-on experience with the analysis of data from various sequencing platforms and applications. Subjects are control of quantity and quality of data, analysis of small RNA-seq and mRNA-seq, de novo genome assembly, and variant calling.

All participants should have a basic understanding of molecular biology, at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. If you are uncertain if your biology background is strong enough, please contact the course coordinators (see contact details below) at least three weeks before the start of the course.

No prior background in bioinformatics or computer science is required, however, we expect students to have a basic understanding of the unix shell. For this, we organise an introductory unix course about a week before the course starts, see the schedule below - details will be provided upon acceptance. Participants who are familiar with the shell can ask to be excempt for this course day.

## Fall 2014 schedule

Monday - Thursday from 9:00 to 16:00 (teachers will stay until 17:00), some lectures, mostly hands-on exercises. All lecture material and most of the practical will be added here.

NOTE The schedule below is tentative, and may be changed prior to the course.

Morning

9:00 - 12:00

Afternoon

13:00 - 17:00

Monday September 22 Unix pre-course for people new to the unix command-line (TR, LN) Unix pre-course for people new to the unix command-line (TR, LN)

Monday October 6

Tuesday October 7 miRNA (MMW) miRNA (MMW)
Wednesday October 8 miRNA (MMW) miRNA (MMW)
Thursday October 9 de novo Assembly (LN) de novo Assembly (LN)
Friday October 10 Day off Day off

Monday October 13 de novo Assembly (LN) de novo Assembly (LN)
Tuesday October 14 How to become a efficient bioinformatician (lectures, discussions). Link to the program. How to become a efficient bioinformatician (lectures, discussions) Link to the program.
Wednesday October 15 RNA-seq (SL, CC) RNA-seq (SL, CC)
Thursday October 16

RNA-seq (SL, CC)

RNA-seq (SL, CC)
Friday October 17

Day off

Day off

Monday October 20 ChIP-seq (DF) ChIP-seq (DF)
Tuesday October 21 Variant calling (TH) Variant calling (TH)
Wednesday October 22 Variant calling (TH) Variant calling (TH)
Thursday October 23 Statistical genomics (SG) Statistical genomics (SG)
Course wrap-up
Friday October 24 Day off Day off

Thursday November 6 Written exam (time and place to be determined)
Friday November 7 Oral exam (time and place to be determined) Oral exam (time and place to be determined)

## Contact information

Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no

Karin Lagesen (Course co-coordinator) - e-mail: karin.lagesen - at - medisin.uio.no

## Teachers

Lex Nederbragt (LN, Norwegian Sequencing Centre, Dept. of Biosciences/Dept. of Informatics, University of Oslo)
Karin Lagesen (KL, Norwegian Sequencing Centre, Oslo Univ. Hospital/Dept. of Informatics)
Daniel Vodák (DV, Bioinformatics core facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Leonardo A. Meza-Zepeda (LMZ, Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Merete Molton Worren (MMW, Bioinformatics core facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Susanne Lorenz (SL, Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Sveinung Gundersen (SG, ELIXIR.NO / The Genomic HyperBrowser team, Dept. of Informatics, University of Oslo)
Timothy Hughes (TH, Norwegian Sequencing Centre, Oslo Univ. Hospital)
Thomas Röblitz (TR, Research Computing Services Group, USIT, University of Oslo)
Katerina Michalickova (KM, Research Computing Services Group, USIT, University of Oslo)
Chandra Sekhar Reddy Chilamakuri (CC, Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
David Fredman (DF, Norwegian Bioinformatics Platform, University of Bergen)

## Computers/laptops, internet access, and UiO user account

All students will be provided with a Linux environment with all software pre-installed. UiO accounts are needed to complete the course. If you don't have a UiO account, please contact karin.lagesen at medisin.uio.no ASAP after having been accepted for the course.

Analysis is done on a remote server. Some data needs to be accessed on the PC's in the course room. Also, students may want to obtain a copy on their own PC for later reference:
• all users: use WinSCP, Fetch, Filezilla, Cyberduck or another such program. Fill in the server details (bioinfcourse.hpc.uio.no) and your username and password. A window will open with files/folder on the local PC on the left, files/folder on the server on the right. Simply drag-and-drop files between the two.
• Linux and Mac users: you can also use the command line. Open a terminal window, navigate to the folder you want to data to be copied to and use this command:
rsync -av YOUR_USERNAME@bioinfcourse.hpc.uio.no:/path/to/data/on/server/files .
• NOTE the '.' at the end of the command, which stands for 'the current folder'

The curriculum consists of a set of scientific articles. The exam will contain questions on the material presented in these papers.

NOTE: reading these papers are optional for non-credit students, however, having read them will make what we teach in the course a lot more understandable.

Specific details of the curriculum, and a list of further suggested papers, can be found here.

## Exam

For students taking the course for 10 study points, the exam for this course will be

• a written exam on the curriculum on November 6th, time and place to be announced
• an individualhome exam combined with an oral examination of the home exam on November 7th. Students will present their work to two-three teachers, followed by some questioning (20-30 minutes in total). This home exam will be handed out to all participants during the last course day.

NOTE Both exams have to be passed to earn 10 study credits.

NOTE  80% attendance is required to take the final exam.

## Bioinformatics mailing list for the Oslo region

The mailing list for computational biology and bioinformatics in the Oslo region is cbo-all@usit.uio.no. The list has approximately 400 members. The list is used to distribute news about seminars, positions, courses, meetings and other topics that might be of interest to students and researchers with an interest in computational life science in south-eastern Norway. If you want to receive e-mails that are sent to the list, sign up here by following the link termed "Subscribe".

Trond Hasle Amundsen's "Local guide to Linux and Unix"

Community resources:

• seqwiki: overview of HTS analysis software, providers, etc
• the 'Next Generation Sequencing' wikibook