I have done the differential accessibility analysis then annotated the region with chipseeker.

my output for one of the many region and question regarding this

Peak log2FoldChange         padj seqnames    start      end width strand        annotation geneChr geneStart
105  Peak32946      -1.992474 9.197721e-19    chr11 14078815 14079558   744      * Distal Intergenic      11  13962689
5445 Peak32938      -2.473959 4.878995e-04    chr11 13961467 13961818   352      *          Promoter      11  13962689
      geneEnd geneLength geneStrand geneId      transcriptId distanceToTSS         ENSEMBL SYMBOL  GENENAME
105  14267884     305196          1  10418 ENST00000576479.3        116126 ENSG00000262655  SPON1 spondin 1
5445 14267884     305196          1  10418 ENST00000576479.3          -871 ENSG00000262655  SPON1 spondin 1

So the same region is marked as Distal Intergenic and Promoter. Next I have the same comparison RNA seq expression data. So now my objective is to find those genes+region which are expressed as well as deferentially accessible.

So for example here in this case in RNA seq data there is only one SPON1 gene so if I have to show it associated region how to put that,shall I consider promoter or the distal intergenic or consider which is more significant.


1 Answer 1


You have two different peaks at different positions with different annotations. This makes complete sense, you're just misreading it.

  • $\begingroup$ "you're just misreading it." this part I got it the gene got two different binding sites. So if i have to find if the accessibility correlates to the expression shall i consider both of them such as taking the mean ? $\endgroup$
    – kcm
    Aug 28, 2021 at 21:53
  • 2
    $\begingroup$ Does it make biological sense to average them? No, it does not. Which is biologically more likely to have an effect? The answer to that will tell you what to do. $\endgroup$
    – Devon Ryan
    Aug 29, 2021 at 8:09

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