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For my PhD I've been looking into DNase-seq analysis, particularly with regards to footprinting (identifying protein-DNA interactions), and was surprised that there was no standard software for doing this sort of analysis. Even the big ENCODE data dump last year didn't release the software used for their footprinting analysis (at least they released the BED files!).
My colleaugues and I have just publsihed a paper describing a fast and efficient footprinting algorithm, and have released a software implementation of it along with an API called pyDNase, which will hopefully make it easier for people to do their own analysis of DNase-seq data.
Let me know if you have any comments or suggestions
J
My colleaugues and I have just publsihed a paper describing a fast and efficient footprinting algorithm, and have released a software implementation of it along with an API called pyDNase, which will hopefully make it easier for people to do their own analysis of DNase-seq data.
Let me know if you have any comments or suggestions
J