Mapping

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# Mapping

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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [](/archive/2019-02-07/topics)

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### <i class="fa fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- What two things are crucial for a correct mapping?

- What is BAM?

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### <i class="fa fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- You will learn what mapping is

- A genome browser is shown that helps you to understand your data

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# What is mapping?

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# Mapping

- Search the position of a read in the genome

![alt text](../../images/igv_mapping.png "IGV Browser")

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# Sequence alignment

```
A A C C G C C T T

A G G G G C C T T

1 2 3 4 5 6 7 8 9
```

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# Sequence alignment

1 2 3 4 5 6 7 8 9
```

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# Looks easy...

Lego time: Who wants to volunteer?

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- Know your data!
- Maybe not the "best" result is the one you are searching for
- Try different mappers

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## Tools, tools, tools

- Bowtie
- HISAT
- MAQ
- BWA
- Eland
- SOAP
- STAR
- BISMARCK

And many more!

???

# Hands-on!

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# SAM/BAM file format

![alt text](../../images/bam_file.png "SAM/BAM file")

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# SAM/BAM file format

![alt text](../../images/bam_file_explained.png "SAM/BAM file detail")

SAM: Sequence Alignment/Map format

BAM: Binary SAM

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# IGV Browser -- Hands-on

![alt text](../../images/igv_part2.png "igv detail")

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### <i class="fa fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points

- Know your data!

- Mapping is not trivial

- There are many mapping algorithms, it depends on your data which one to choose

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## Thank you!

This material is the result of a collaborative work. Thanks the [Galaxy Training Network](https://wiki.galaxyproject.org/Teach/GTN) and all the contributors  (Joachim Wolff) !