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Results

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Navigate to the Projects page and select the View button to view the pipeline results.

Output​

The output files are placed into separate folders named after the tool that produced them.

FASTQC​

fastqc is a computer program used to examine the quality of raw sequence data. Standard quality control metrics for each sample can be viewed by downloading the files ending with a .html extension to your computer and opening them in a web browser.

MULTIQC​

multiqc is a computer program also used to examine the quality of raw sequence data. This program aggregates all FASTQC files into a single report that can be easily viewed in a browser.

CELLRANGER​

cellranger is a computer program developed by 10X Genomics that aligns single-cell reads to a reference genome and counts the number of genes within each cell. Single-cell gene counts for each sample are stored in the raw_feature_bc_matrix and filtered_feature_bc_matrix folders.

tip

These two folders contains the output files needed to perform downstream clustering, cell typing and differential gene expression using Seurat in R or ScanPy in Python.

PIPELINE_INFO​

pipeline_info is a folder containing auxillary information about the pipeline:

  • pipeline software (nf_core_rnaseq_software_mqc_versions.yml)
  • pipeline parameters (params_2024-12-20_16-56-03.json)
  • execution report (execution_report_2024-12-20_16-55-39.html)
info

The information included in this folder can be helpful for writing the materials and methods section of your manuscript or grant; and learning more about what is happening under the hood of the pipeline.