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Weeks-UNC / shapemapper2

Public repository for ShapeMapper 2 releases
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masking the primers in shape reactivity profile #41

Open gunjangunjan22 opened 1 year ago

gunjangunjan22 commented 1 year ago

HI I was using shapemapper2 for my analysis. We have three sample experiments i.e., denatured, modified, and untreated. I ran the experiments by giving the primer sequences in lowercase in input.fa file with --amplicon feature. I got the shape profile, I have .map and .shape with the reactivity value -999 at primer sites. but I want to trim the reactivity profile of primers in my .shape and .map files. I checked the deltaSHAPE.py script, but it requires two map files, which I don't have. Can you please help in masking the reactivity profile of primers in my data

Psirving commented 1 year ago

You want to remove the primer regions? You could just remove them from the input.fa and re-run Shapemapper2.

Psirving commented 1 year ago

deltaSHAPE.py is for comparing an in-cell and a cell-free probing experiment to detect protein binding. It requires 2 experiments. You'll need to run Shapemapper2 on each of these experiments to get 2 .map files.

gunjangunjan22 commented 1 year ago

Thanks for responding. I have tried this but this had not solved my issue. I have tried removing primers with bbtools, but the reactivity profile always have some primer regions in it. but i can always retry once.

gunjangunjan22 commented 1 year ago

I have run my samples as you have said but it changes the reactivity profile if I compare to the file that I got from run with primers.