Output

The Pipeline creates different types of data. The data is sorted in Folders and Subfolders inside the output directory.

Structure

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 found 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.
log	Every step creates a log-file which is stored in the log directory of each step directory.