The following directories will be created in the current directory after the pipeline has finished.
Nextflow's output (report.html, timeline.html, trace.txt and dag.dot).
| Directory | Description |
|---|---|
quality_control/fastqc/raw/ |
FastQC results before adapter trimming |
quality_control/fastqc/cutadapt/ |
FastQC results after adapter trimming |
quality_control/picard/ |
Picard metrics |
quality_control/rnaseqc/ |
RNA-SeQC metrics |
quality_control/rnaseqc/ |
RSeQC package metrics |
quality_control/multiqc_report.html/ |
MultiQC report of all the metrics |
| Directory | Description |
|---|---|
results/analysis/ |
count matrix and PCA results |
results/cutadapt/ |
trimmed FASTQ files from cutadapt |
results/rsem/ |
results of the alignment from RSEM and STAR |