http://denver.cbslocal.com/2013/02/13/colorado-researchers-say-dna-proves-bigfoot-is-real/
So you're saying there is a problem distinguishing unknown DNA from just a bad sample? This may be a reason why DNA from Bigfoot is so hard to sequence. We have nothing to compare it to.
There is a problem if the material is bad, in which case there's no primer hybridization. I recall something about the "Starchild" - a Mesoamerican skull with severe hydrocephaly - that was called 'alien' for a long time. The nuclear DNA was unusable due to age, but the mtDNA had survived - this is normal, since mtDNA is smaller than genomic and more stable in that sense - so the owners took to insisting that the 'starchild' had a human mother since mtDNA is passed on maternally. Negative evidence was turned into oblique positive evidence - lacking only the point that with a human mother, you'd still be able to pull out the maternal (human) nuclear haplotype.
Unless Alien Dad's haplotype was so possessive about Starchild's mom's DNA that it bound it up with weird bonding patterns that prevented cDNA hybridization. Could be; aliens do seem to have that thing about human womenfolk.

Er... uh, not that I, personally, would know anything about that. I have kidnapped none of your womenfolk and I stand by that sketchy assertion.