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/

Description

Directory	Description
./out/cluster/	Contains Output from clustering.
./out/estimated_motifs/unknown_motifs/	Contains possible de novo motifs as MEME-files
./out/estimated_motifs/clustered_motifs/	Contains subfolder for each cluster, which contain the output from GLAM2
./out/estimated_motifs/clustered_motifs/clustered_fasta/	Contains the FASTA-file for each cluster
./out/final_estimated_motifs/	Contains output from motif clustering, if activated
./out/footprint_extraction/	Contains output from footprint extraction
./out/footprint_extraction/log/	Contains the log-file from footprint extraction
/out/unknown_overlap/	Contains the output from overlapping footprints with known motifs
/out/gtf/	Contains from pipeline build gtf-file