Does the bigwig file of a single-end chip-seq shows 2 peaks for a fragment whereas the paired-end show one peak ?
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?
• 786 views
•
link
updated
by
Ram
•
written
by
Rajendra KC •
•
written
by
Rajendra KC •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Cross-strand correlation for paired-end ChIP-seq data
written by alison.ludzki •
-
Optimal MACS2/3 configuration for paired-end ChIP-seq data: `-f BAM` versus `-f BAMPE`
written by kalavattam •
-
making a BIGWIG from BAM file
written by Rajendra KC •
-
Paired End RIP-seq analysis with MACS2 reasonable parameters?
written by ddierks91 •
-
Normalizing ChIP-seq and ATAC-seq data?
written by star
-
Peak call? or Just convert to bedfile by bedtools bamtobed? to generate the accessibility matrix of…
written by soya •
-
Bam to BigWig loss of data at MACS peaks (nothing in the BigWig why?)
written by contreras.xavier •
-
Strange peaks in paired-end ChIP-Seq independent on Abs but not single-end or input
written by greulich.fr •
-
Best way to map paired-end, uniquely mapped reads with Bowtie2?
written by Ian
-
Is There Any Advantage Of Paired End Sequencing For Chip-Seq?
written by Fidel
