I am hoping for some insight and suggestions :)
I am interested in the TFBSs of 3 TFs in all promoter sequences of the human genome (e.g. 1000bp upstream) - in particular, I am looking for co-occurring TFBSs of these 3 TFs. I have the motifs available through the JASPAR database.
I found following solutions:
FIMO (Meme Suite) & findMotifs.pl or scanMotifGenomeWide.pl (HOMER) offer a way of scanning for them using known motifs. Each motif is treated separately – I then computed the co-occurring ones in R.
MCAST (Meme Suite) offers to scan for clusters (however it gives any clusters not co-occurring specifically and very few results … and occasionally segmentation fault, so I dropped it). Is there another tool that scans for co-occurring TFBSs is particular?
JASPAR offers a pre-scanned genome based on FIMO and TFBS Perl module - so I subsetted with the predictions of TFs of interest and the regions of interest (promoters).
REMAP 2018: offers merged peaks across ChIP-seq experiments for many TFs. Assuming that most binding sites are shared in different cell types / conditions, one could use these - correct? Again, I subsetted with the peaks of TFs of interest and the regions of interest (promoters). Unfortunately, not all TFs I am interested in are in this database. Any other similar resources available?
I am grateful for any insight: remarks to my solutions, other tools, other solutions, reviews on this problem ... anything :)