Question 1 1 pts You have 100 reads for exon 3 in gene A. You know a priori that

Question

Question 1 1 pts You have 100 reads for exon 3 in gene A. You know a priori that this exon is used in 3 isoforms. How do you determine how many reads in exon 3 originate from isoform A.1? 1/3 of the reads come from isoform A.1 (33 reads). You can never be fully sure, but with information on the other exons and splice junctions you can attempt to infer it. Only one isoform is expressed per cell type, so you have to determine which one of these isoforms is expressed in this experiment (so answer is 0 or 100) DQuestion 2 1 pts You use ChlP-seq to identify the binding sites of your favorite transcription factor, p53. A colleague who is studying colon cancer walks into your office incredulous that your list fails to find a p53 binding site in front of his favorite gene, gut1. You promise to double check your analysis of your ChIP and find that directly over the promoter of gut1 there is a small region with 25 reads in your ChIP-e IP sample. What happened? Your peak caller must have something wrong with it because it didn't find this region This region is clearly not bound by p53 You should check the background (whole cell extract) sample first in this region before making any conclusions Just change the parameters to your peak caller until it finds this peak

Explanation / Answer

Question no. 1.

Answer: b

Explanation: It can never be confirmed but information of other exon and splice junction will help to infer it. Option a and c have wrong information.

Question no. 2.

Answer: c

Explanation: To improve the accuracy of CHIP-Seq experiment, background checking is very important. It will help to detect non-specific binding and improve peak signal.

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