Output inteprate

Result Folder structure

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

Result
├── Alignment
│   ├── Bowtie2
│   │   └── bowtie2_unmapped_S483_T_chrX_R.bam
│   ├── BWA
│   │   └── bwa_S483_T_chrX_R.mem.sam
│   └── STAR
│       └── star_S483_T_chrX_R_Chimeric.out.junction
├── circRNA_Identification
│   ├── CIRCexplorer2
│   │   ├── circexplorer2_merge.matrix
│   │   ├── CIRCexplorer2_S483_T_chrX_R_circularRNA_known.txt
│   │   └── S483_T_chrX_R_modify_circexplorer2.candidates.bed
│   ├── CIRI
│   │   ├── ciri_merge.matrix
│   │   ├── CIRI_S483_T_chrX_R.txt
│   │   └── S483_T_chrX_R_modify_ciri.candidates.bed
│   ├── Find_circ
│   │   ├── find_circ_merge.matrix
│   │   ├── find_circ_S483_T_chrX_R_splice_sites.bed
│   │   └── S483_T_chrX_R_modify_finc_circ.candidates.bed
│   ├── Mapsplice
│   │   ├── mapsplice_merge.matrix
│   │   ├── output_mapsplice_S483_T_chrX_R
│   │   │   ├── alignments.sam
│   │   │   ├── circular_RNAs.txt
│   │   │   ├── deletions.txt
│   │   │   ├── fusions_candidates.txt
│   │   │   ├── fusions_not_well_annotated.txt
│   │   │   ├── fusions_raw.txt
│   │   │   ├── fusions_well_annotated.txt
│   │   │   ├── insertions.txt
│   │   │   ├── junctions.txt
│   │   │   ├── logs
│   │   │   │   ├── add_fusion_strand_consistent.err
│   │   │   │   ├── add_fusion_strand_consistent.log
│   │   │   │   ├── alignment_handler_fusion.err
│   │   │   │   ├── alignment_handler_fusion.log
│   │   │   │   ├── alignment_handler_remap.err
│   │   │   │   ├── alignment_handler_remap.log
│   │   │   │   ├── anchor_bowtie.err
│   │   │   │   ├── anchor_bowtie.log
│   │   │   │   ├── annotate_fusion.log
│   │   │   │   ├── best_junction_semi_non_canon_remained_ROC.log
│   │   │   │   ├── bowtie_build.log
│   │   │   │   ├── bowtie_refnames
│   │   │   │   ├── check_reads_format.log
│   │   │   │   ├── collectstats.log
│   │   │   │   ├── FilterFusionByNormalPaired.log
│   │   │   │   ├── FilterFusionSamByFusionJunc.log
│   │   │   │   ├── filterremappedfusion.log
│   │   │   │   ├── fusion_junc_db.log
│   │   │   │   ├── fusionsam2junc_original_fusion_junction.log
│   │   │   │   ├── fusionsam2junc_remapped_fusion_junction.log
│   │   │   │   ├── fusion_unmapped.1_2sam.log
│   │   │   │   ├── fusion_unmapped.2_2sam.log
│   │   │   │   ├── gtf2genetab.log
│   │   │   │   ├── junc_db.log
│   │   │   │   ├── load_fusion_chrom_seq_std.log
│   │   │   │   ├── load_fusion_chrom_seq_std_long_seq.log
│   │   │   │   ├── long_fusion_seq_bowtie.err
│   │   │   │   ├── long_fusion_seq_bowtie.log
│   │   │   │   ├── mapsplice_fusion.log
│   │   │   │   ├── mapsplice_fusion_original.log
│   │   │   │   ├── mapsplice_original.log
│   │   │   │   ├── mapsplice_remap.log
│   │   │   │   ├── matchfusion2normal.log
│   │   │   │   ├── ori.all_junctions_filtered_by_min_mis_lpq.log
│   │   │   │   ├── ori.filteroriginalfusion.log
│   │   │   │   ├── pair_repeat_reads.err
│   │   │   │   ├── pair_repeat_reads.log
│   │   │   │   ├── read_chromo_sizes.log
│   │   │   │   ├── remap_cluster.log
│   │   │   │   ├── remap_parseCluster.log
│   │   │   │   ├── sam2junc_ori.all_junctions.log
│   │   │   │   ├── SeparateNormalFromFusionJunc.log
│   │   │   │   ├── SetUnmappedBitFlag.log
│   │   │   │   └── sort_repeat.log
│   │   │   └── stats.txt
│   │   ├── S483_T_chrX_R_mapsplice.log
│   │   └── S483_T_chrX_R_modify_mapsplice.candidates.bed
│   └── Segemehl
│       ├── S483_T_chrX_R_modify_segemehl.candidates.bed
│       ├── segemehl_merge.matrix
│       └── segemehl_S483_T_chrX_R_splicesites.bed
├── Combination_Matrix
│   ├── all_tools_merge.matrix
│   └── final.matrix
├── Annotation
│   ├── merge_for_annotation_annote.txt
│   ├── merge_venn.png  
│   ├── merge_distribution.png 
│   ├── merge_spanningtree.png 
│   ├── merge_hist.png 
│   ├── merge_circos.png 
│   └── merge_calculates.pdf
├── DE_Analysis
│   ├── merge_volcano.png 
│   ├── merge_heatmap1.png 
│   ├── merge_heatmap2.png 
│   ├── merge_heatmap3.png 
│   ├── merge_pca1.png 
│   ├── merge_pca2.png
│   └── merge_plots.pdf
├── Correlation_Analysis
└── QC
    ├── multiqc_report.html
    └── S483_T_chrX_R_fastpreport.html

• QC stored the Quality control output generated by Fastp software.
  
• circRNA_Identification contains all assembled circRNAs and their sequences. *.candidates.bed is the standard bed6 format of the known circRNAs; *.matrix is the matrix of all samples gene expression.
  
• Alignment are BWA/Bowtie2/STAR aligner outputs.
  
• Combination_Matrix stores the matrix merge from all the selected tools. final.matrix stored the expression matrix and all_tools_merge.matrix show whether the tools are detected in this gene.
  
• Annoation stores the information of the circRNAs annotation.
  
• DE_Analysis stores the information of the circRNAs differential expression.
  
• Correlation_Analysis stores the information of the circRNAs correlation analysis.
  

Output directory: Result/QC

• S483_T_chrX_R_fastpreport.html
  • Fastp report of raw fastq files
• multiqc_report.html
  • merge of all Fastp report

Output directory: Result/Combination_Matrix

• final.matrix
  • the expression matrix of all samples
• all_tools_merge.matrix
  • the information of whether the tools are detected in this gene

Output directory: Result/Alignment

• *.bam
  • alignment result in bam format.
• *.sam
  • alignment result in sam format.

Output directory: Result/circRNA_Identification

• *.candidates.bed

  • the standard bed6 format of the known circRNAs.

• *.matrix

  • the matrix of all samples gene expression of the specific pipelines.

Output directory: Result/Annoation

• the information of the circRNAs annotation.

Output directory: Result/DE_Analysis

• the information of the circRNAs differential expression.

Output directory: Result/Correlation_Analysis

• the information of the circRNAs correlation analysis.

Notes about the results

All bed format from the circpipe are 0-based coordinates. CIRI and Mapsplice outoupt are 1-based but have been transformed into 0-based coordinates for consistency.