Fragments file format

[Colin]

Hi,

I used createFitHiCFragments-fixedsize.py to generate the fragments input file, but it doesn't match what's described in the documentation. Instead, I get a bed output (instead of fragment midpoint), plus "1" in the 4th and 5th fields.

Is this a mistake or am I misunderstanding something? I'm also confused because the docs say the fragments file should contain a number of counts associated with each fragment, while that is not an input for createFitHiCFragments-fixedsize.py (only needs chromosome sizes + resolution).

Thanks!

Colin

[Ferhat Ay]

The file you should be getting should look like this:

chr extraField fragmentMid marginalizedContactCount mappable? (0/1)
1 0 15000 234 1

... 

And among these 5 fields, only critical ones are chr and fragmentMid. second field doesn't matter. fourth field is not important unless you want to specifically filter with respect to this number (problematic ones will be filtered through bias filter anyhow).

fifth field is similar to fourth, mostly overwritten by bias filtering. 

So I would assume you are in good shape. Please try running it and see.

Thanks

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