Sirius through car AUX input-clicking noise

I have a sportster replay which was giving me static problems when using the now weaker FM transmitter. It was recommended that I try running an audio cable from the sportster directly into my car's aux. input. It solved the static, but there is a definite "clicking" noise through the radio. I've been told this is probably electrical interference from the alternator, or other parts of the electrical system. Has anyone heard of this?? Could a better quality audio cable help eliminate this noise (i'm using a pretty cheap cable) ?? I thought a direct connection was supposed to give "crystal clear" sound quality...Any help would be greatly appreciated.