Update README.md

README.md

@@ -61,34 +61,52 @@ Command-line examples
 These examples use the test data provided in the [TOBIAS/test_data](https://github.molgen.mpg.de/loosolab/TOBIAS/tree/master/test_data) directory, so please make sure you are in the upper TOBIAS/ directory when running the commands.
 
 **ATACorrect: Bias correction of ATAC-seq reads in open chromatin**     
-`TOBIAS ATACorrect --bam test_data/Bcell_chr4.bam --genome test_data/genome_chr4.fa.gz --peaks test_data/merged_peaks.bed --blacklist test_data/blacklist_chr4.bed --outdir atacorrect_test --prefix Bcell --cores 8`
+```
+$ TOBIAS ATACorrect --bam test_data/Bcell_chr4.bam --genome test_data/genome_chr4.fa.gz --peaks test_data/merged_peaks.bed --blacklist test_data/blacklist_chr4.bed --outdir atacorrect_test --prefix Bcell --cores 8
+```
 
-**FootprintScores: Calculate footprint scores from corrected cutsites**    
-`TOBIAS FootprintScores --signal test_data/Bcell_corrected.bw --regions test_data/merged_peaks.bed --output Bcell_footprints.bw --cores 8`
+**FootprintScores: Calculate footprint scores from corrected cutsites**
+```
+$ TOBIAS FootprintScores --signal test_data/Bcell_corrected.bw --regions test_data/merged_peaks.bed --output Bcell_footprints.bw --cores 8
+```
 
 **BINDetect: Estimation of differentially bound motifs based on scores, sequence and motifs**   
-`TOBIAS BINDetect --motifs test_data/example_motifs.txt --signals test_data/Bcell_footprints.bw test_data/Tcell_footprints.bw --genome test_data/genome_chr4.fa.gz --peaks test_data/annotated_peaks.bed --peak_header test_data/annotated_peaks_header.txt --outdir bindetect_output --cond_names Bcell Tcell --cores 8`
+```
+$ TOBIAS BINDetect --motifs test_data/example_motifs.txt --signals test_data/Bcell_footprints.bw test_data/Tcell_footprints.bw --genome test_data/genome_chr4.fa.gz --peaks test_data/annotated_peaks.bed --peak_header test_data/annotated_peaks_header.txt --outdir bindetect_output --cond_names Bcell Tcell --cores 8
+```
 
 **PlotAggregate: Plot aggregated ATAC-seq signals in combinations of .bed/.bw to visualize footprints**  
 
 Visualize the difference in footprints between two conditions for all accessible sites:    
-`TOBIAS PlotAggregate --TFBS test_data/BATFJUN_all.bed  --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_footprint_comparison_all.pdf --share_y both --plot_boundaries`
+```
+$ TOBIAS PlotAggregate --TFBS test_data/BATFJUN_all.bed  --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_footprint_comparison_all.pdf --share_y both --plot_boundaries
+```
 
 Visualize the difference in footprints between two conditions exclusively for bound sites:   
-`TOBIAS PlotAggregate --TFBS test_data/BATFJUN_Bcell_bound.bed test_data/BATFJUN_Tcell_bound.bed --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_footprint_comparison_subsets.pdf --share_y both --plot_boundaries`   
+```
+$ TOBIAS PlotAggregate --TFBS test_data/BATFJUN_Bcell_bound.bed test_data/BATFJUN_Tcell_bound.bed --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_footprint_comparison_subsets.pdf --share_y both --plot_boundaries
+```
 
 Visualize the split of bound/unbound sites for one condition:   
-`TOBIAS PlotAggregate --TFBS test_data/IRF1_all.bed test_data/IRF1_bound.bed test_data/IRF1_unbound.bed --signals test_data/Bcell_uncorrected.bw test_data/Bcell_expected.bw test_data/Bcell_corrected.bw --output IRF1_footprint.pdf  --share_y rows --plot_boundaries`
+```
+$ TOBIAS PlotAggregate --TFBS test_data/IRF1_all.bed test_data/IRF1_bound.bed test_data/IRF1_unbound.bed --signals test_data/Bcell_uncorrected.bw test_data/Bcell_expected.bw test_data/Bcell_corrected.bw --output IRF1_footprint.pdf  --share_y rows --plot_boundaries
+```
 
 **PlotHeatmap: Plot heatmaps and aggregates of ATAC-seq signals in combinations of .bed/.bw to visualize footprints**   
-``TOBIAS PlotHeatmap --TFBS test_data/BATFJUN_Bcell_bound.bed test_data/BATFJUN_Bcell_unbound.bed --TFBS test_data/BATFJUN_Tcell_bound.bed test_data/BATFJUN_Tcell_unbound.bed --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_heatmap.pdf --signal_labels Bcell Tcell --share_colorbar``
+```
+$ TOBIAS PlotHeatmap --TFBS test_data/BATFJUN_Bcell_bound.bed test_data/BATFJUN_Bcell_unbound.bed --TFBS test_data/BATFJUN_Tcell_bound.bed test_data/BATFJUN_Tcell_unbound.bed --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_heatmap.pdf --signal_labels Bcell Tcell --share_colorbar
+```
 
 **FormatMotifs: A utility to convert and join/split across different motif-file formats**    
 Join individual motif files to one:    
-`TOBIAS FormatMotifs --input test_data/individual_motifs/* --format pfm --task join --output example_motifs.txt`  
+```
+$ TOBIAS FormatMotifs --input test_data/individual_motifs/* --format pfm --task join --output example_motifs.txt
+```
 
 Split a motif file containing several motifs:    
-`TOBIAS FormatMotifs --input test_data/example_motifs.txt --format pfm --task split --output split_motifs`
+```
+$ TOBIAS FormatMotifs --input test_data/example_motifs.txt --format pfm --task split --output split_motifs
+```
 
 
 Snakemake pipeline