---
title: "CUTANA™ Cloud Quick Start Guide"
slug: "cutana-cloud-quick-start-guide"
tags: ["cut and run", "cut and tag", "Tutorial", "Getting started"]
updated: 2026-11-13T17:05:49Z
published: 2026-11-13T16:53:40Z
canonical: "support.epicypher.com/cutana-cloud-quick-start-guide"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://support.epicypher.com/llms.txt
> Use this file to discover all available pages before exploring further.

# CUTANA™ Cloud Quick Start Guide

## 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](mailto:techsupport@epicypher.com). Our team is happy to recommend the best output files for your application.