Additional

Cluster Motifs: Cluster motifs and create consensus motifs based on similarity

$ TOBIAS ClusterMotifs --motifs test_data/motifs.jaspar --threshold 0.4 --type png

Filter fragments from a .bam-file using a .bed-file of regions:

$ TOBIAS FilterFragments --bam test_data/Bcell.bam --regions test_data/merged_peaks.bed

Merge pdf files to one

$ TOBIAS MergePDF --input test_data/*_footprint_comparison_all.pdf --output joined.pdf

Score .bed-file with signal from .bigwig-file(s)

$ TOBIAS ScoreBed --bed test_data/merged_peaks.bed --bigwigs test_data/Bcell_corrected.bw --output merged_peaks_scored.bed

Get .bed-positions of highest bigwig signal within .bed-regions

$ TOBIAS MaxPos --bed test_data/merged_peaks.bed --bigwig test_data/Bcell_footprints.bw --output merged_peaks_max.bed

Subsample a .bam-file using samtools

$ TOBIAS SubsampleBam --bam test_data/Bcell.bam --no_rand 1 --step 50 --outdir subsamplebam_output

Convert logs from PlotAggregate to tab-delimitered tables of footprint stats

$ TOBIAS Log2Table --logfiles test_data/BATF_footprint_comparison_all.log --outdir log2table_output

Plot changes in TF binding across multiple conditions (from BINDetect output)

$ echo 'CTCF KLF4 GATA NFAT MEF2 NR2F1 ETS NRF1 ELK ATF' > TF_names.txt
$ TOBIAS PlotChanges --bindetect test_data/Tcell_bindetect_results.txt --TFS TF_names.txt

Identify positions of TFBS given sequence and motifs

$ TOBIAS TFBScan --motifs test_data/motifs.jaspar --fasta test_data/genome.fa.gz --cores 10
$ TOBIAS TFBScan --motifs test_data/motifs.jaspar --fasta test_data/genome.fa.gz --cores 10 --regions test_data/merged_peaks_annotated.bed --add-region-columns