No, if your knees are actually bothering you then you don't want to keep just powering through on the squats. I would recommend either what I said IF it is comfortable..which is just messing around and adding some reps to the 3 by 5 set for a bit until and IF the knee feels better and meanwhile put in the pullthroughs because they should be OK I think as far as the knee.
Another option is to go to box squats for a bit because provided they are done right they are easier on the knees.
And there is always the option of dropping the squat for something else for a bit.
You know, I'm sure Rip would say do this little tweak or that tweak and then work the ass end off your knees until they miraculously adapt, lol. But ain't nobody gonna be coming around giving your free rehab services when things go south so you have to do what is comfortable for you.
I certainly would also recommend doing some appropriate stretches if you aren't already doing them. For example ITB. And some foam rolling. Lots of guys around here can give you the hook up on that.
All this sounds complicated but it's really not. Let pain be your guide but I'm sure this is just a normal "growing" pain you'll have to work around.
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