Program to detect cis-regulatory modules for a non model species?

Question

[DNAngel]

Hi all,

Initially I wanted to use the program Stubb along with cis-Metalysis to ultimately detect enriched TFs in my species.

However, the program Stubb is so old it does not compile on any computer or cluster that we have. Stubb was written in 2003 so it is very old unfortunately and doesn't appear to be maintained. There is another program called SWAN which does something similar, but links to that are also broken and also cause many errors when being used

I have been stuck on this for over a month. Other programs I've come across such as MEME or I-cisTarget appear to already require a list of factors or binding sites, which we are trying to find in the first place.

Does anyone have a pipeline that works for non-model species (not fruitfly/zebrafish/human). As reference, I am working on a bee (and not honeybees).

Any advice or tips or links to tutorials/alternative programs that do what I am asking would be SO great and I thank you so much for all your help.

Answer 1

[colindaven]

Seems like a big ask to just do this computationally. I don't think authors should be expected to support tools written 20 years ago - are you doing the same things you were doing 20 years ago, I'm not.

Please mention any data you have:

• methylation (if appropriate in your bee species)
• chip-seq
• public data from closely related species
• repeat annotation
• gene annotation

To be honest though, projects like modENCODE among many others have generated a wealth of data for eg human and mouse, but regulation in these species is anything but solved. I face similar problems in my non-model plants.

[DNAngel]

It is RNA extraction using Illumina NovaSeq. Gene annotation was done as well (although many genes are uncharacterized proteins).