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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.

FASTP​

fastp is a read trimmer used to remove technical artifacts introduced during sequencing (e.g., primers and adapters) and low quality base pairs. The trimmed sequence data is used as input for downstream analysis like sequence alignment and transcript quantification.

MIRNA_QUANT​

mirna_quant module uses a computer program called Bowtie to align sequence reads to a miRNA reference database: miRBase or MirGeneDB. The count matrix storing the number of hits to each miRNA sequence is stored in the mirna.tsv file.

tip

This directory contains the output files needed to perform downstream data visualization and statistical analysis. These files can be directly loaded into R or RStudio and analyzed using your favorite software packages.

GENOME_QUANT​

genome_quant module uses Bowtie to align sequence reads to a user-specified host reference genome to identify novel miRNA sequences. The output of this module is a collection of BAM files.

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.