Results
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Navigate to the Projects page and select the Result 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.
TRIMGALORE
trimgalore 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.
SALMON
salmon is a pseudo-alignment program used for transcript and gene quantification from a reference genome. Transcript and gene-level counts for each sample are stored in the quant.sf and quant.genes.sf files.
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.
STAR_SALMON
star_salmon is a sequence alignment program used to compare sequence data to a reference genome. The output of this program is a collection of BAM files that can be viewed within a genome browser or as the starting point for additional analyses.
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)
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.