Hello, everyone!

I'm new to bioinformatics and I'm currently working on a research project for school. I was originally a wet lab person working with cancer cells, but I was forced to switch to a bioinformatics project because of the pandemic. Most of the tools I have to work with weren't taught in class and everyone in the lab I belong to is too busy to guide me for the process remotely, meaning I'm learning everything on my own.

I was hoping I could get some advice from you guys with how to go about the project.

To put it simply, my project has two main objectives:

1.) To confirm the presence of androgen response elements in regions with overlaps between the peaks found in the ChIP-seq data of two interacting proteins (one of which is the androgen receptor)
2.) To identify the genes that could be regulated by the co-binding of said proteins and make inferences on the overall effects of the co-binding through a gene ontology analysis

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My planned workflow is something like this:

1.) Get the overlapping regions of the peaks from two ChIP-seq data sets (Output: BED file with the overlapping regions)
2.) List the genes that either flank the overlapping regions (<1000 kbp distance) or overlap with them

3.) Label these genes and identify whether they're upregulated or downregulated by the AR using RNA-seq data

4.) Do a gene ontology analysis using the generated gene list

5.) Look for androgen response elements in the overlapping region. And also maybe look for enriched TF binding sites in those regions

6.) Consolidate all the data and make inferences regarding the interaction of the two proteins and contextualize it based on the gene ontology results and existing literature

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To be honest, I'm not even sure which tools I should use from steps 2 to 6, let alone how to use them. I know it's a lot, but if anyone could offer me some advice, I'd greatly appreciate it.