If you have followed the generic instructions for the RGT suite installation, then you can start using HINT.
If you have any questions, comments, installation problems or bug reports, please access our discussion group.
Note: You must download the genomic data for bias correction.
Download here. Execute the following commands in order to perform footprints identification from DNase–seq data:
cd HINT_DNaseTest rgt-hint --dnase-footprints --output-location=./ --output-prefix=test DNase.bam DNasePeaks.bed
The above commands will output a BED file containing the footprints, inside the current folder with test as the prefix. Each footprint, i.e. each line of the BED file, will also contain information regarding the tag-count score of each footprint. This score can be used as a footprint quality assessment (the higher the value, the better). In addition, a file including the details of reads and footprints will also be written in the same folder of BED file.
Complete tutorial and more descriptive examples are found in here.
If you use HINT/HINT-BC in your research, please cite the following publication:
Gusmao EG, Allhoff M, Zenke M and Costa IG. “Analysis of computational footprinting methods for DNase sequencing experiments”. Nature Methods, 13(4):303-309, 2016.[Full Text]
Gusmao EG, Dieterich C, Zenke M and Costa IG. “Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications” Bioinformatics, 30(22):3143-3151, 2014. [Full Text]