Chipseq peak calling and peak frequency region
Entering edit mode
3 months ago
mavy ▴ 10

I am working on Chip seq data, I have implemented the chipseq pipeline with spike in method and called peaks using MACS2.

The same data has been analyzed before in my lab, and my peaks show a similar pattern as the previous ones . By this I meant that the samples showing more peaks before are showing more in mine too. (which I consider that my work till peak calling is correct)

Now I have to do the downstream analysis, for which I am using CHipseeker R package.

I am plotting the number of peaks around the TSS, it shows the maximum peak frequency at the TSS , whereas the previous results indicate that they are minimum at the TSS and also proven in the text.

I am completely clueless about what I am doing wrong or what's causing this difference.

I am using the .broadpeak file from its output as the bed files input in the Chipseeker package. Am I using the wrong bed file ??

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

promoter <- getPromoters(TxDb=txdb, upstream=2000, downstream=2000)

tagMatrixList <- lapply(files, getTagMatrix, windows=promoter)

plotAvgProf(tagMatrixList, xlim=c(-3000, 3000), conf=0.95,resample=500, facet="row")

Will appreciate any help regarding this

chipseeker macs2 • 298 views
Entering edit mode

If you are working with Histone modification data the broadpeak file is the right choice for TF binding events choose narrowPeak.


Login before adding your answer.

Traffic: 2709 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6