- Introduction: Quick Start, Tutorial, Flowchart, Outputs structure
- Install: Dependencies, Containers, References, Test datasets
- Inputs: Data, Design, Parameters
- 1. Preprocessing: ATAC reads, ATAC peaks, mRNA
- 2. Differential Analysis: ATAC, mRNA, Split
- 3. Enrichment Analysis: Enrichment, Figures, Tables
Quantification of transcripts abundance is made with kallisto in single or paired-end mode according to the input type. Briefly, Kallisto is based on the recent idea of a pseudoalignment that allows fasta and precise alignment-free quantification of transcripts (more details here).
- params.kallisto__nb_threads: number of threads used by kallisto. Default: 6.
- params.kallisto__bootstrap: Number of bootstrap samples. Default: '100'.
- params.kallisto__fragment_len: Estimated average fragment length. For single end only. Default: '180'.
- params.kallisto__fragment_sd: Estimated standard deviation of fragment length. For single end only. Default: '20'.
- Kallisto results:
Processed_Data/1_Preprocessing/mRNA__kallisto_output/kallisto_${sample}/{abundance.{h5,tsv},run_info.json}.
FastQC is runned to perform standard quality controls checks on sequenced data.
- params.fastqc__nb_threads: number of threads used by FastQC. Default: 2.
- Reads quality control reports:
Processed_Data/1_Preprocessing/mRNA__fastqc/*_R{1,2}_fastqc.html.
A MultiQC html report is made that aggregates all basic FastQC quality controls files.
- MultiQC report:
mRNA__multiQC.html. Example.
Figures_Individual/1_PreprocessingFigures_Merged/1_Preprocessing