Input files and how to get them

Hello,

I am trying to run CHiCAGO to incorporate it in our capture HiC analysis pipelines. I am having some trouble with my input files and would like to understand how to get the files in the correct format.

Here is my current understanding: I will need 6 files, as follows:

1- restriction map file (.rmap)

2- Baitmap file (.baitmap)

3- nperbin file (.npb)

4- nbaitsperbin file (.nbpb)

5- proxOE file (.poe)

6- input file (.chinput)

What I have:

-bam aligned by HiCUP

-HiCUP digest file

-bait coordinates

My understanding is that I can get files 3,4,5 by running makeDesignFiles.py but I will need .rmap and .baitmap.

I can also get file 6 by using bam2chicago.sh. but I also need .rmap and .baitmap.

So i am missing files 1 and 2 (.rmap, .baitmap) and am wondering how to get those. Are there scripts to do so?

I thought I can make the .rmap file by taking the first 3 columns of the HiCUP digest file and assigning an arbitrary "numeric ID" and I can make the .baitmap from the 3 first columns of the chip bait coordinates and an arbitrary "numeric ID". but I am confused by the following comment in the README.md file " [bait coordinates] (should be a subset of the fragments listed in rmapfile), their numeric IDs (should match those listed in rmapfile for the corresponding fragments)".

Is there a better way to produce the .rmap and .baitmap files and how do I coordinate the ID of the rmap file with those in the baitmap file?

Thank you, Rola

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