Entering edit mode
19 months ago
Rajendra KC
▴
20
My thinking goes like this. In a single-end chip-seq, there will be accumulation of reads in either side of any putative fragment of DNA so I feel the bigwig file will also show peaks at both the end of the fragment. However, in paired-end chip-seq , Bowtie(or any other alignment tools) will merge the paired reads situated at the two sides of a fragment and mark as a single big read in bam file, and thus the bigwig file will probably show a single peak at the center of the putative fragment.
Am I correct?