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renewiegandt edited this page Apr 12, 2019 · 9 revisions
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The Pipeline creates different types of data. The data is sorted in Folders and Subfolders inside the output directory.

Structure

  • ./out
    • /1.1_footprint_extraction
      • /log/
    • /1.2_filter_motifs
      • /compareBed/
    • /2.1_clustering
      • /reduced_bed/
      • /log/
    • /2.2_motif_estimation
      • /log/
      • /glam2/
      • /tomtom/
      • /fasta/
      • /best_unknown_motifs
        • /motif_sequences/
    • /3.1_create_gtf/
    • /3.2_evaluation
      • /rescan/
      • /uropa
        • /config/
        • /summary/
      • /venn/

Description

Directory Description
./out//1.1_footprint_extraction Contains the output of step 1.1 footprint extraction.
./out//1.2_filter_motifs/compareBed Contains the output of Step 1.2 filtermotifs.
./out//2.1_clustering Contains output of step 2.1 clustering.
./out/2.1_clustering/reduced_bed/ Contains the BED-file with reduced sequences before clustering.
./out/2.2_motif_estimation Contains the output from step 2.2 motif estimation.
./out/2.2_motif_estimation/glam2 Contains a directory for each cluster, which contain the output of GLAM2
./out/2.2_motif_estimation/tomtom Contains a tsv-file for each cluster. If tomtom finds no similarity with a motif in the database the file only contains the header.
./out/2.2_motif_estimation/fasta Contains the FASTA-file created from each cluster
./out/2.2_motif_estimation/best_unknown_motifs Contains the MEME-files of each cluster. Each MEME-file contains the X (Default: 3) motifs with the highest score.
./out/2.2_motif_estimation/best_unknown_motifs/motif_sequences Contains a JSON-file for each file in best_unknown_motif. The JSON-file contains the sequence names used to create each motif.
/out/3.1_create_gtf Contains from pipeline build GTF-file.
/out/3.2_evaluation/rescan/ Contains the BED-files with regions found by scanning the genome on the new motifs
/out/3.2_evaluation/uropa/ Contains the output generated by uropa + all config files + the summarys for each uropa run
/out/3.2_evaluation/venn/ PDF-files containing the venn diagrams
log Every log file from the run is stored here.