Output Interpretations

Result Folder structure

Result folder under current path(default) or output_folder set by user. A typical structure of Result is follows:

Result
├── aligners
│   └── star/bwa/hisat2/tophat2
├── peak_calling
│   ├── macs2
│   │   ├── macs2_A_group_A_normalized.bed
│   │   └── ...
│   ├── metpeak
│   │   ├── metpeak_A_group_A_normalized.bed
│   │   └── ...
│   ├── meyer
│   │   ├── meyer_A_group_A_normalized.bed
│   │   └── ...
│   └── matk
│       ├── matk_A_group_A_normalized.bed
│       └── ...
├── QC
│   ├── fastp
│   ├── fastqc
│   ├── rseqc
│   └── multiqc
├── samtools_sort
│   └── sample_rename
│       └── bam_for_resume
└── result_arranged
    ├── annotation
    ├── diff_expression
    │   ├── htseq_count
    │   └── edgeR/deseq2
    ├── diffm6A
    ├── m6A_prediction_sites
    ├── merged_bed
    ├── motif
    ├── quantification
    └── final_results

• aligners are STAR/BWA/Hisat2/Tophat2 aligner outputs.
  
• peak_calling stored the PeakCalling results of the four options tools.
  
• QC stored Quality Control output generated by Fastp, FastQC, RSeQC and MultiQC.
  
• samtools_sort contains all aligned reads of data, which are sorted (BAM files); sample_rename is rename of sorted BAM files for downstream analysis; bam_for_resume is rename of sorted BAM files for using the last designfile to resume the pipeline, in order to transfer generated results for other clusters.
  
• result_arranged stores the analysis results including expression analysis (diff_expression), merge peaks by RobustRankAggreg (merged_bed), methylation analysis (quantification & diffm6A), prediction of m6A sites (m6A_prediction_sites), motif search (motif).
  

Output directory: results/QC

• fastp
  • Store the results of Fastp.
• fastqc
  • Store the results of FastQC.
• rseqc
  • Store the results of RSeQC.
• multiqc
  • Store the results of MultiQC.

Output directory: results/samtools_sort

• sample_rename
  • Store sorted renamed BAM files for downstream analysis.
• bam_for_resume
  • Store sorted renamed BAM files for resume the pipeline without Alignment.

Output directory: results/aligners/star(bwa/hisat2/tophat2)

• *.bam
  • alignment result in bam format.

Output directory: results/peak_calling

• macs2
  • macs2*.normalized.bed are the peaks called by macs2, whose P-value is converted to log2(P-value).
• metpeak
  • metpeak*.normalized.bed are the peaks called by MeTPeak, which transfer bed12 format into bed6 format and P-value is converted into log2(P-value).
• meyer
  • meyer*.normalized.bed are the peaks called by Meyer, whose P-value is converted to log2(P-value).
• matk
  • matk*.normalized.bed are the peaks called by MATK, whose P-value is converted to log2(P-value).

Output directory: results/results_arranged

• Store the analysis results of m6APipe