When cutting up the jalapeño, can I leave the seeds in them if I just lay them on a tray, freeze, then put them in my Seal a Meal? Do you think I need to blanch them, and if so can I leave the seeds in?

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You can certainly leave the seeds in (there is no food safety issue), but the peppers themselves will be affected by the freezing. Peppers have a tendency to be somewhat mushy when thawed out. That's usually fine in when they are cooked or put in something soft, but may not be great on something like nachos. Blanching is only needed if you want to peel the peppers or if you're cooking them after thawing them anyway.

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