Question

In ChIP-seq cross-correlation, what are X and Y in the context of Pearson's correlation coefficient?

a. X is the Watson strand, Y is the Crick strand
b. X is the count of reads, Y is the distance
c. X is the fragment length, Y is the correlation value
d. X is the correlation value, Y is the read position

Why does sequencing-by-synthesis result in ChIP-seq reads primarily at the 5' ends of DNA strands?

a. DNA synthesis follows a 5'->3' direction
b. Reads are obtained from both 3' and 5' ends
c. Fragment ends are chemically modified
d. Sequencing technology favors 5' ends

What does the artefactual phantom peak in ChIP-seq cross-correlation refer to?

a. Read length variation
b. Fragment length variation
c. Correlation between strands
d. Biased alignment towards the 3' end

Why might fragment length introduce a signal in cross-correlation, and what is the primary quantity of interest in the method?

a. Fragment length introduces read duplication
b. Fragment length affects library complexity
c. Fragment length indicates alignment bias
d. Fragment length is the primary interest, especially average length

Answer 1

In ChIP-seq cross-correlation, X represents the fragment length and Y represents the correlation value. Sequencing-by-synthesis results in ChIP-seq reads primarily at the 5' ends of DNA strands, and the artefactual phantom peak in ChIP-seq cross-correlation refers to a biased alignment towards the 3' end.

Step-by-step explanation:

In ChIP-seq cross-correlation, X represents the fragment length, while Y represents the correlation value. The fragment length refers to the size of the DNA fragments that are sequenced, and the correlation value indicates the degree of similarity or association between the two strands of DNA being analyzed.

Sequencing-by-synthesis results in ChIP-seq reads primarily at the 5' ends of DNA strands because DNA synthesis follows a 5'->3' direction. This means that the sequencing technology starts synthesizing the DNA strand from the 5' end, resulting in reads primarily being obtained from the 5' ends.

The artefactual phantom peak in ChIP-seq cross-correlation refers to a biased alignment towards the 3' end. It indicates that there is an artificial peak in the cross-correlation analysis, which can be caused by biases in the alignment of the sequencing reads towards the 3' end of the DNA strands.