- 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
Here are some considerations:
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File format: Input data files should be .fastq.gz files.
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Replication: There should be at least 2 replicates per conditions.
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Library type:
- Data must be paired-end for ATAC-Seq.
- Data can be either paired-end or single-end for mRNA-Seq.
- Paired-end data files should end with "R1.fastq.gz" or "R2.fastq.gz".
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Merging samples: Different sequencing runs of the same sample/replicate can be automatically merged by cactus (see the Design section to see how).