Downloading Individual and Bulk Analysis Files
Once your analysis has completed, CUTANA™ Cloud makes it easy to download individual output files or export multiple files at once for downstream analysis, visualization, or archival.
Step 1: Open Your Completed Analysis
From the project page, verify your analysis status is Complete, then navigate to the All Files section in the left-hand navigation.
At the root of your project you'll see two primary folders:
Input: Contains uploaded FASTQ files and input data.
Output: Contains all analysis results generated by CUTANA™ Cloud.
Tip: All downloadable analysis results are located within the Output folder.
Step 2: Navigate to the Output Folder
Open the following folder hierarchy:
Output → example alignment
Inside you'll see folders such as:
FASTQs
Alignment Job
FastQC
Select the Alignment Job folder.
Step 3: Select Your Genome Build
Each genome analyzed will have its own folder (example: Human hg19). Open the appropriate genome folder for your experiment.
Step 4: Choose the Type of Results
Within the genome folder you'll find two primary directories: 01_Reports and 02_Alignment_Output.
01_Reports contains summary reports, including:
Alignment Summary Report (.html)
methods.txt
These files are useful for:
Reviewing experiment QC
Sharing reports with collaborators
Publication methods
02_Alignment_Output contains all processed analysis files used for downstream analysis. Open this folder to access your data products.
Step 5: Browse Analysis Outputs
Within 02_Alignment_Output you'll find several folders, including:
2.1 Seq Stats
2.2 Unique BAM
2.3 Genome Wide Heatmaps
2.4 IGV Smoothed BigWig
2.5 Intermediate Alignment Files
2.6 Spike-ins (when applicable)
Each folder contains files specific to that stage of the workflow.
Step 6: Select Files to Download
Navigate into the folder containing the files you need.
For example:
2.2 Unique BAM
Select one or multiple files by checking the box next to each filename.
The interface will display the number of selected items near the top of the page.
Example:
4 Items Selected
Step 7: Download Your Files
After selecting your files, click the Download button in the upper-right corner. CUTANA™ Cloud will display a Download Data window showing:
Selected filenames
Individual file sizes
Total download size
Review your selection and click Download All. Your browser will begin downloading the selected files.
Common Output Files
File Type | Purpose |
Alignment Summary Report (.html) | Interactive QC summary of your experiment |
methods.txt | Analysis methods and pipeline information |
Final BAM (.bam) | Recommended aligned reads for downstream analysis |
BAM Index (.bai) | Required index file for viewing BAM files in IGV |
BigWig (.bw) | Signal tracks for genome browser visualization |
Peak Files (.bed) | Peak coordinates for downstream bioinformatics analyses |
Heatmaps | Genome-wide enrichment visualizations |
Recommended Downloads
For IGV Visualization
Download:
Final BAM (.bam)
BAM Index (.bai)
Both files should remain in the same directory on your computer for proper loading into IGV.
For Publication
We recommend downloading:
Alignment Summary Report
Final BAM
BigWig
Peak Files
methods.txt
These files provide the QC metrics, visualization tracks, and methods documentation commonly used for publications.
For Tertiary Bioinformatics Analysis
Depending on your workflow, you may wish to download:
Final BAM
Peak Files
BigWig
Intermediate Alignment Files (if additional custom analyses are planned)
Tips
* Use Ctrl (Windows) or ⌘ Command (Mac) to select multiple individual files.
* Select an entire folder to download all contents at once.
* Larger downloads may take several minutes to prepare before downloading.
* Keep .bam and .bai files together to ensure compatibility with genome browsers such as IGV.
Need Help?
If you're unsure which files are appropriate for your downstream analysis or publication, contact techsupport@epicypher.com. Our team is happy to recommend the best output files for your application.