In Variant Detection, RNA-sequencing, and ChIP-sequencing, we showed how we matching, or aligning, short NGS reads to the genome, and then make inference using the reads which aggregate or "pile up" at a given region: either to find a SNP, to quantify the amount of mRNA, or the quantify the amount of a protein which is bound to DNA. Define a "true positive" as detecting a SNP, detecting mRNA expression, or detecting a protein which is bound to DNA. Which of the following (you can pick more than one) could possibly lead to a false negative, e.g. we do not detect a true SNP, mRNA expression, or a bound protein at a location/region?
which one is the correct answer? why? (we can pick more than one)
1.The region we care about is not in the reference genome
2.The region we care about occurs 1000s of times in the genome, and we are ignoring reads which align to so many places
3.For the region we care about, the organism's genome is so different to the reference genome that the aligning program can't find a match
4.There are never false positives