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MalteThodberg / CAGEfightR

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
GNU General Public License v3.0
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bidirectional promoters #16

Open jtxyz16 opened 1 year ago

jtxyz16 commented 1 year ago

not an issue but a general inquiry. Can one use clusterBidirectionally to map bidirectional promoters? bidirectional promoters are classically defined as 1kb regions between 2 opposite TSSs(+ and - strand TSSs). Can I reliably use the 'subset promoter' to isolate the bidirectional promoters based on the above definition? Thanks for your help.

MalteThodberg commented 1 year ago

I haven't tried that specifically, but clusterBidirectionally should detect any bidirectionally transcribed region. The default window size might not be appropriate though, as that was set with locating enhancers in mind. Once you have bidirectional clusters, you can use assignTxType to overlap with known promoters.

Since promoter TSSs are much more highly expressed, I suspect there could be other more obvious ways of finding bidirectional promoters though - for example just looking at highly expressed tag clusters and find bidirectional pairs within some distance.