ft footprint yaml file explanation

[yaroslovakia]

Hello!

I would like to use fibertools to find footprints of TFs in my FiberSeq data and I can not understand what is meant by yaml file in your documentation. Could you please explain how it should be created and what is meant by multiple binding sites?

Thank you in advance

[mrvollger]

Hi there,

I can expand but need some direction first on what you find confusing about the yaml input: https://fiberseq.github.io/fibertools/extracting/footprint.html
Can you elaborate?

[yaroslovakia]

I do not understand what are modules in yaml file. In your example:

modules:

• [0, 8]
• [8, 16]
• [16, 23]
• [23, 29]
• [29, 35]

How to define these modules for every TF?

[mrvollger]

For example, we used literature to find the binding modes of CTCF as it doesn't always bind the whole motif:

https://pubmed.ncbi.nlm.nih.gov/24614316/

So each module is a different part of sequence that can be bound individually by your TF.

If you are unsure of the modules of your TF, looking are raw data can be helpful. Or simplifying to a single module in the yaml.

[yaroslovakia]

Thank you for the explanation!

I have tried to use ft footprint for CTCF ChIP-Seq bed file with your example yaml file. I recieved this error

Error: Motif length in the BED record (197) does not match to the total length (35) in the footprint YAML:
chr1 16148 16345 CTCF_v2_peak_1 311 . 12.5408 33.8912 31.1755 94

Could you please explain what is wrong? Maybe the error arises because of my bed file.