Extended regulatory circuitry

[mkunika]

Hello,

My lab is interested in predicting an extended regulatory circuit to the CRC we narrowed down from CRCmapper. I am very much a beginner in bioinformatics, and understanding and being able to manipulate the CRCmapper source code has been challenging. From reading through the source code and the supplementary methods from CRCmapper's corresponding paper (PMC4772020), I gather that I can use the _SUBPEAKS.fa file containing extended SE constituents to search for genes that have motif instances predicting the binding of our candidate core TFs. However, it is to my understanding the _SUBPEAKS.fa file does not contain the TSS region or extended typical enhancer constituents--both of which are mentioned to be used for motif search to predict the extended circuit. How can I obtain a bed or fasta file containing the TSS region and the extended typical enhancer consistuents?

Also, could you provide any advice or guidance on how to modify the motif searching section of the script to search for genes with motif instances of ~5 candidate core TFs?

I would appreciate any help! Thank you!