<commit_before>Title: The Shell and the Cloud - Applied Bioinformatics on the Example of Gene Expression Analysis using Unix and freely available Open Source Tools</br>
Author: <NAME></br>
EMail: ak at silico-sciences.com</br>
Seminar Ruprecht-Karls-Universität Heidelberg 2016-01-20 - 2016-01-22

# Applied Bioinformatics in the Shell and in the Cloud

## NGS Data Analysis Using Unix and Open Source Tools

# RNA-Seq using Galaxy, IGV and the Tuxedo Suite

0. Get familar with your tools.
[Galaxy](https://usegalaxy.org/)

    0. Create user account.

    0. Learn how to rename datasets.
    
    0. Learn how to change dataset attributes.
    
    0. Learn how to use Histories.
    
    0. Take a look at the [Wiki](https://github.com/nekrut/galaxy/wiki).

0. Get familiar with your data.
[ENA, Study ERP003613](http://www.ebi.ac.uk/ena/data/view/ERP003613)

    Since NGS data analysis is usually very time consumng, in this tutorial we will use a smaller data set. It has been reduced to chromosome 3 only to save some time and disk space.

0. Load the [reference sequence](../2014fagerberg-small/3.fa.gz?raw=true) into Galaxy.

    ![note](../figs/note_20x20.png) It is not necessary to download files on your computer first, Galaxy can get them directly. Just copy the link and paste the URLs into the Galaxy upload wizard.

    ![note](../figs/attention_22x20.png) If you experience problems with Copy&Paste'ed download links, please import the following history: https://usegalaxy.org/u/kerner1000/h/2014fagerberg-small
    
    0. Edit data attributes:
        
        0. Change datatype to `fasta`.
        
0. Load the [reference annotation](../2014fagerberg-small/genes_chr03.gtf.gz?raw=true) into Galaxy. The annotation should be in [GTF format](http://www.ensembl.org/info/website/upload/gff.html).

0. Load [small data sets](https://github.com/silico-sciences/bi-seminar/tree/master/2014fagerberg-small) into Galaxy. Each tissues was sequenced in four replicates and each replicates has one file for the forward reads (`_1.fastq`) and reverse reads (`_2.fastq`).

    0. [lung1-4_1](../2014fagerberg-small/lung/ERR315326/ERR315326_chr03_1.fastq?raw=true)
    0. [lung1-4_2](../2014fagerberg-small/lung/ERR315326/ERR315326_chr03_2.fastq?raw=true)
    0. [lung2-4_1](../2014fagerberg-small/lung/ERR315326/ERR315341_chr03_1.fastq?raw=true)
    0. [lung2-4_2](../2014fagerberg-small/lung/ERR315326/ERR315341_chr03_2.fastq?raw=true)
    0. [lung3-4_1](../2014fagerberg-small/lung/ERR315326/ERR315346_chr03_1.fastq?raw=true)
    0. [lung3-4_2](../2014fagerberg-small/lung/ERR315326/ERR315346_chr03_2.fastq?raw=true)
    0. [lung4-4_1](../2014fagerberg-small/lung/ERR315326/ERR315353_chr03_1.fastq?raw=true)
    0. [lung4-4_2](../2014fagerberg-small/lung/ERR315326/ERR315353_chr03_2.fastq?raw=true)

    0. Edit data attributes:
        
        0. Change datatype to `fastqsanger`.<commit_msg>Continue<commit_after>Title: The Shell and the Cloud - Applied Bioinformatics on the Example of Gene Expression Analysis using Unix and freely available Open Source Tools</br>
Author: <NAME></br>
EMail: ak at silico-sciences.com</br>
Seminar Ruprecht-Karls-Universität Heidelberg 2016-01-20 - 2016-01-22

# Applied Bioinformatics in the Shell and in the Cloud

## NGS Data Analysis Using Unix and Open Source Tools

# RNA-Seq using Galaxy, IGV and the Tuxedo Suite

0. Get familar with your tools.
[Galaxy](https://usegalaxy.org/)

    0. Create user account.

    0. Learn how to rename datasets.
    
    0. Learn how to change dataset attributes.
    
    0. Learn how to use Histories.
    
    0. Take a look at the [Wiki](https://github.com/nekrut/galaxy/wiki).

0. Get familiar with your data.
[ENA, Study ERP003613](http://www.ebi.ac.uk/ena/data/view/ERP003613)

    Since NGS data analysis is usually very time consumng, in this tutorial we will use a smaller data set. It has been reduced to chromosome 3 only to save some time and disk space.

0. Load the [reference sequence](../2014fagerberg-small/3.fa.gz?raw=true) into Galaxy.

    ![note](../figs/note_20x20.png) It is not necessary to download files on your computer first, Galaxy can get them directly. Just copy the link and paste the URLs into the Galaxy upload wizard.

    ![note](../figs/attention_22x20.png) If you experience problems with Copy&Paste'ed download links, please import the following history: https://usegalaxy.org/u/kerner1000/h/2014fagerberg-small
    
    0. Edit data attributes:
        
        0. Change datatype to `fasta`.
        
0. Load the [reference annotation](../2014fagerberg-small/genes_chr03.gtf.gz?raw=true) into Galaxy.

    0. The annotation should be in [GTF format](http://www.ensembl.org/info/website/upload/gff.html).

0. Load [small data sets](https://github.com/silico-sciences/bi-seminar/tree/master/2014fagerberg-small) into Galaxy. Each tissues was sequenced in four replicates and each replicates has one file for the forward reads (`_1.fastq`) and reverse reads (`_2.fastq`).

    0. [lung1-4_1](../2014fagerberg-small/lung/ERR315326/ERR315326_chr03_1.fastq?raw=true)
    0. [lung1-4_2](../2014fagerberg-small/lung/ERR315326/ERR315326_chr03_2.fastq?raw=true)
    0. [lung2-4_1](../2014fagerberg-small/lung/ERR315326/ERR315341_chr03_1.fastq?raw=true)
    0. [lung2-4_2](../2014fagerberg-small/lung/ERR315326/ERR315341_chr03_2.fastq?raw=true)
    0. [lung3-4_1](../2014fagerberg-small/lung/ERR315326/ERR315346_chr03_1.fastq?raw=true)
    0. [lung3-4_2](../2014fagerberg-small/lung/ERR315326/ERR315346_chr03_2.fastq?raw=true)
    0. [lung4-4_1](../2014fagerberg-small/lung/ERR315326/ERR315353_chr03_1.fastq?raw=true)
    0. [lung4-4_2](../2014fagerberg-small/lung/ERR315326/ERR315353_chr03_2.fastq?raw=true)

    0. Edit data attributes:
        
        0. Change datatype to `fastqsanger`.
{'fraction_non_alphanumeric': 0.11539122957867584, 'fraction_numerical': 0.08959587274290627, 'mean_word_length': 3.6528, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 11, 'https://': 8, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '497808', 'n_tokens_mistral': 2315, 'n_tokens_neox': 1954, 'n_words': 538}