Output

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.