Does the bigwig file of a single-end chip-seq shows 2 peaks for a fragment whereas the paired-end show one peak ?
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13 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?

peak chip-seq bigwig single-end • 351 views
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