Weeks-UNC/shapemapper2

masking the primers in shape reactivity profile

gunjangunjan22 opened this issue · 4 comments

gunjangunjan22 commented

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

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

Psirving commented

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

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

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.