Mapping I: Intro

Course: HT17 Analysis-of-next-generation-sequencing-data (SC00024)

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The purpose of this exercise is to introduce you to some common aligners and understand that you should be familiar with the data to be analyzed in order to pick the right tool.

Your task is to run different tools for mapping sequencing data (BWA, Bowtie2, TopHat and STAR) generate some statistics (samtools, picard) and visualize the alignments using IGV.

Write a report where you shortly describe the differences/advantages/drawbacks of the different tools. Justify any preference towards any of the tools.

Answers to marked questions with a 'Q', are for you to explore different output files, you do not need to include them in the report

The Data

For these exercises, we will be using data from samples AS_2 (exome) from this paper and Ctrl1 (RNAseq) that target chr21 from ENA (ERR1523942)

The server

Connect to the server using MobaXterm (PC users) or your local Terminal (MACS users):

ssh -X your_account@rudy.biomedicine.gu.se

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Next: Mapping II: Aligners