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Your cyst that you are having on your inner thigh might require incision and drainage and oral and topical antibiotics before it will completely go away. When these 'cyst' reoccur like this, it is best to have them surgically drained and treated. The area you have described on your backside is often called a pilonidal cyst. This occurs because a small amount of debris, hair, or bacteria get lodged and becomes infected. This actually affects men more than women. You can click here for more about pilonidal cyst.
If you continue to have slight pain/irritation down the left side of your penis and it does not resolve on it's own in a few days or gets worse or you start to develop new symptoms (such as painful urination), it would be a good idea to let your GP know in case they want to examine you.
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Yes, it can be common to have a cyst in this area and this might be where your pain is coming from. You have lymph nodes in this area and if infection is nearby, you could be having pain from the infection that is not resolved. I would recommend that you see your GP as soon as you get the chance.