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Output
renewiegandt edited this page Apr 12, 2019
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The Pipeline creates different types of data. The data is sorted in Folders and Subfolders inside the output directory.
- ./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/
- /1.1_footprint_extraction
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. |