IMPORT DATA IN YOUR GALAXY ACCOUNT

1. Introduction

For the course "Analyse des Génomes", we need three types of datasets

• The reference sequences that will be used to align sequencing reads (full genome, miRNA, transposons, etc.)
• libraries of sequencing reads from small RNAs (for analysis of piRNAs)
• Librairies of sequencing reads from mRNA (for Gene differential expression analysis)

2. Galaxy data library

All of this data has been pre-loaded into the Bibliothèque de données (Data Library) on your Galaxy server. You can access it from the menu by navigating to Data → Bibliothèque de données.

In this data library, you'll see three subfolders.

Fasta and GTF references

• dmel-r6.59-clean.fa → The "clean" dmel reference genome, version 6.59 (BDGP). "Clean" means that only the main main chromosomes are kept (excluding haplotypes and unassembled contigs) and were renamed with short names: 2L, 2R, 3L, 3R, 4, X and Y.
• dmel-r6.59-gtf → The corresponding genome annotation in GTF format.
• dmel-r6.59-miRNA → the pre-miRNA sequences in fasta format.
• dmel-r6.59-miscRNA → Sequences of snoRNAs, snRNA and, importantly, of rRNAs, in fasta format.
• dmel-r6.59-tRNA → The pre-tRNA sequences (before processing and editing) in fasta format.
• PLacZ → The sequence of the PLacZ transgene

RNAseq datasets

• GLKD-ALBA1 → sequence reads of RNAseq library from a GLKD mutant sample (replicat-1); FASTQ format.
• GLKD-ALBA2 → sequence reads of RNAseq library from a GLKD mutant sample (replicat-2); FASTQ format.
• GLKD-ALBA3 → sequence reads of RNAseq library from a GLKD mutant sample (replicat-3); FASTQ format.
• WT-ALBA4 → sequence reads of RNAseq library from a WT sample (replicat-1); FASTQ format.
• WT-ALBA5 → sequence reads of RNAseq library from a WT sample (replicat-2); FASTQ format.
• WT-ALBA6 → sequence reads of RNAseq library from a WT sample (replicat-3); FASTQ format.
• Test-Mapping → a sample of sequence reads that you will use for tests; FASTQ format.

Small RNAseq datasets

• GLKD-ALBA28 → sequence reads of small RNAseq library from a GLKD mutant sample (replicat-1); FASTQ format.
• GLKD-ALBA29 → sequence reads of small RNAseq library from a GLKD mutant sample (replicat-2); FASTQ format.
• GLKD-ALBA30 → sequence reads of small RNAseq library from a GLKD mutant sample (replicat-3); FASTQ format.
• WT-ALBA25 → sequence reads of small RNAseq library from a WT sample (replicat-1); FASTQ format.
• WT-ALBA26 → sequence reads of small RNAseq library from a WT sample (replicat-2); FASTQ format.
• WT-ALBA27 → sequence reads of small RNAseq library from a WT sample (replicat-3); FASTQ format.

3. Dataset Library usage

When you need one or more datasets for an analysis, import* them from the Data Library into a new or pre-existing Galaxy history.

Below we give you four examples of imports from the Data Library.

A. Import references datasets into your pre-existing Unnamed history

• 1. Go to Data → Bibliothèque de données.
• 2. Click Fasta and GTF references.
• 3. Check all boxes before the datasets.
• 4. In the top menu Add to History, select as Datasets.
• 5. In the popup panel, leave the Select history to Unnamed history and click Import.
• → Now, you'll see the three selected dataset showing up in the Unnamed history.

Before the next step, rename the history Unamed history to References by clicking the small icon to the right of the history name.

B. Import RNAseq datasets into a new history named RNAseq libraries

• 1. Go to Data → Bibliothèque de données.
• 2. Click RNAseq datasets.
• 3. Check the boxes before GLKD-ALBA1, GLKD-ALBA2 and GLKD-ALBA3
• 4. In the top menu Add to History, select as Datasets.
• 5. In the popup panel, type RNAseq Analysis in the or create new: field and click Import.
• → Now, you'll see the three selected dataset showing up in a new history named RNAseq libraries.

C. Import RNAseq datasets as a collection into the RNAseq Analysis history

• 1. Go to Data → Bibliothèque de données.
• 2. Click RNAseq datasets.
• 3. Check the boxes before WT-ALBA4, WT-ALBA5 and WT-ALBA6.
• 4. In the top menu Add to History, select as Collection.
• 5. In the popup panel, leave Collection type as List, ensure that Select history is RNAseq Analysis and click Continue.
• 6. In the new panel Create a collection from a list of datasets, you can reorder the 3-element collection. Give it the name WT RNAseq datasets, and click the Create collection button.
• → Now, you'll see a collection of the three selected dataset showing up in the RNAseq libraries history. You can click on this collection and see the three contained datasets. Click on the << History link, to come back to the normal history view.

C. Import small RNAseq datasets into the new small RNAseq Analysis history

• 1. Go to Data → Bibliothèque de données.
• 2. Click Small RNAseq datasets.
• 3. Check all boxes before the datasets.
• 4. In the top menu Add to History, select as Datasets.
• 5. In the popup panel, type small RNAseq Analysis in the or create new: field and click Import.
• → Now, you'll see the six selected dataset showing up in a new history named small RNAseq Analysis.

4. About datasets collections

A Galaxy Collection is a container object which is convenient to treat together multiple equivalent datasets, such as a list of sequencing datasets, of text labels, of fasta sequences, etc.

Collections are particularly useful for RNAseq datasets, since these datasets often come as replicates which can be grouped upon a label. Your training is indeed a good example of that, since you are provided with 3 WT datasets (ALBA4, 5 and 6) and 3 GLKD datasets (ALBA1, 2 and 3).

You have just created a 3-element collection WT RNAseq datasets, but the three other datasets GLKD... in the history RNAseq Analysis still stand as single datasets.

Here is a procedure to make a collection from these datasets.

• Go to your RNAseq Analysis history. There are multiple ways to this; Here, just click on the double arrow icon and select the RNAseq Analysis history.

• In the history RNAseq Analysis, click the upper left small check box at the top of the dataset stack .

• Check the 3 datasets GLKD (-ALBA1, 2 and 3)

• From the menu 3 of 4 selected (in dark blue,top area of the history), select Build Dataset List

  

• In the pop-up panel, type Mutant RNAseq datasets in the field Name: Enter a name for your new collection

• Reorganize the datasets order by clicking the alphabetic sorting icon.
• Press the button Create Collection

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