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The tutorial data set includes 9 samples equally divided into 3 treatment groups. Sequencing was performed by an Illumina HiSeq (paired-end reads), but the workflow can be easily adapted for data generated by other sequencers. Each sample has 2 fastq files for a total of 18 fastq files with the combined size of 6.17 GB.
This tutorial will use two sets of samples: human brain reference (HBR) samples and universal human reference (UHR) samples (five each). Data was generated using an Ion Torrent® sequencer (single-end chemistry), but the workflow can be easily adapted for data generated by sequencers from other manufacturers. The project consists of 10 fastq files with the combined size of 1.4 GB.
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You can obtain the tutorial data set
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through Partek Flow.
- Select your avatar
- Select Settings from the drop-down menu (Figure 1)
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Figure 1.
Partek® Flow®
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At the top of the System information page, there is a section labeled Download tutorial data (Figure 2)
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Figure 2. Downloading
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- Select RNA-Seq 5-AZA to download the tutorial data set
A new project will be created and you will be directed to the Data Tab. The data will be downloaded automatically (Figure 3) and imported into your project.
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Because this is a tutorial project, there is no need to click on Import data as it will be done automatically.
Figure 3. Creating a new project based on a sample data set. The project will be populated with samples automatically
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At first the project is empty, but the file download will start automatically in the background. You can wait a few minutes
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then refresh
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your browser or you can monitor the download progress
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using the Queue.
- Select Queue
- Select View Queued Tasks from the drop-down menu
The Queued tasks page will open (Figure 4)
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Figure 4. Downloading tutorial data task in the queue (note that any user can download sample data set)
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- Select Projects
- Select RNA-Seq 5-AZA from the drop-down menu
The Analyses tab will open (Figure 5). If you download has completed, you will see a blue circle titled Unaligned reads. We will return to this page in the next section of the tutorial.
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We can edit the project name, description, and users who can access it using the Project settings menu.
- Select the Project settings tab
- Select
- Set the name to RNA-Seq Tutorial or whatever you prefer
- Write a brief description; for example, 5-AZA data set
- Select Save
- Refresh your browser
Once the download completes, the sample table will appear in the Data tab.
- Select the Data tab (Figure 5)
The Data tab includes the sample table with the names of each imported sample. There should be 9 samples once the import has completed (Figure 5).
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In the next section of the tutorial, we will add sample attributes that designate the treatment group of each sample.
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