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In this step, we will align our reads to the A. thaliana (TAIR10) reference genome. We will be using HiSAT2-index-align app from the Discovery Environment (DE) that builds a HISAT2 index for your genome and then map the reads.
Input Data:
| Input | Description | Example |
|---|---|---|
| Leaf RNA-seq data | 1M reads dataset from SRR7947123 | iplantcollaborative > example_data > HAMR_tutorial -> fastqfiles |
| Reference Genome |
|
iplantcollaborative > example_data > HAMR_tutorial -> reference_genome |
Run HISAT2 in the CyVerse Discovery Environment
- Click on "Apps" tab in the Discovery Environment and search for "hisat2".
- Click on the app icon HISAT2-index-align-2.1.
- Change the name of the analysis and output folder as needed or leave for defaults.
- Under Input section provide Reference genome file in Fasta format. Browse through the datastore and provide TAIR10_allchr.fasta reference genome. This file is provided with the sample dataset- iplantcollaborative > example_data > HAMR_tutorial -> reference_genome.
- Provide FASTQ files from the path iplantcollaborative > example_data > HAMR_tutorial -> fastqfiles. Choose the File type as PE for this dataset and click launch analysis.
Output/Results
| Output | Description | Example |
|---|---|---|
| Alignment files | Alignment files in BAM format | SRR7947123_1M.sorted.bam |
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