Pre‐Processing Page - bvshvarf/bvshvarf.github.io GitHub Wiki

Pre-Processing Page

Author: James Gillis

The Pre-Processing page is where users begin their journey with DataSeq. This interface lets you upload raw FASTQ data, select a data type, and begin the automated pre-processing pipeline with minimal setup or technical knowledge.

Interface Overview

Below is a screenshot of the Pre-Processing page. This includes the header UI, file upload ui, data type selector ui, and configuration creation UI:

Pre-Processing Interface Screenshot

Tasks You Can Perform

1. Upload a FASTQ File

See file upload task manual here

2. Select a Data Type

  • Choose the type of sequencing data you're processing:
    • RNA-seq
    • ATAC-seq
    • WGBS

This is done with the Datatype Selector UI that utilizes the radio buttons as shown below

Data Type Selector UI

3. Upload or Create a Configuration

See Configuration UI Creation task manual here

4. Begin Pre-Processing

  • After choosing a config and data type, click Sub For Preprocessing.

image

  • This will send over your config file and start the QC step.

image

  • A QC report will be generated to guide potential changes to your configuration file.
  • Afterwards there will be an ID for you to copy to retrieve your pre-processed file on the Downloads page

Return to User Interface Overview