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Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.
I-ATAC / Interactive- Assay for Transposase Accessible Chromatin
Facilitates processing of Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) samples. I-ATAC is an interactive and cross-platform software that aims to facilitate data analysis for scientists generating data. It has been tested on ATAC-seq single and paired end data (in-house and publicly available) at The Jackson Laboratory for Genomics Medicine and UConn Health Center, USA. The software can also be used to perform quality checking and pre-preprocessing of whole genome sequencing (WGS) and ChIP-seq data.
HMMRATAC / Hidden Markov ModeleR for ATAC-seq
Determines open chromatin regions and plausible transcription factor binding sites (TFBS) from single ATAC-seq data. HMMRATAC is based on an algorithm able to consider all the spectrum of the fragment lengths. This application uses a hidden Markov model able to split a dataset into multiple layers standing for different chromatin features and lastly exploits them to rearrange patterns. This application was tested on three standards datasets.
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