comparative peak analysis

Question

[Azhar]

Hi,

I want to compare my TF-DNA binding sites to already available data as well as to see conservation in other species like mouse, rat, monkey etc. How can I do? I need help.

Thanks

Answer 1

[Sam]

Could you provide a little bit more information? I'm assuming you are wanting to compare human data to other species? What exactly are you trying to do? What's your biological question?

One source you might want to take a look at is the Encode Project page (https://www.encodeproject.org/). You'll be able to find a variety of downloadable datasets for different cell types and different transcription factors. Just choose a similar cell type, species and transcription factor as your own and see if there's something you can compare your data too.

If you're asking what methods you can use to 'compare' your data, then we will probably need a little bit more information on what question you are trying to answer specifically.

Deeptools (https://github.com/fidelram/deepTools) might be something to look into, specifically the bamFingerprint option. The tool is useful for preliminary and even deeper analysis visualization.

Conservation analysis is not something I'm very familiar with but you could take a look at the following topics: How To Extract Conserved Regions From A Large Number Of Sequences, Liftover And Sequence Conservation, Measuring Conservation, Ultra-Conservation In Genome Comparisons