After doing peak call I'm annotating the peaks using chipseeker tool, which I want to take further downstream analysis. Now unlike RNA seq where i have single gene and their respective expression. But here the peaks for a single gene multiple peaks. As an example have filtered promoter peaks.
seqnames start end width strand V4 annotation geneChr geneStart geneEnd geneLength geneStrand geneId
1 chr1 826797 828101 1305 * Peak1 Promoter 1 826832 852225 25394 1 643837
2 chr1 869647 870324 678 * Peak4 Promoter 1 868240 870201 1962 2 284593
3 chr1 876462 877140 679 * Peak5 Promoter 1 868071 876903 8833 2 284593
4 chr1 877219 878105 887 * Peak6 Promoter 1 874529 877234 2706 2 284593
5 chr1 923459 924318 860 * Peak14 Promoter 1 923928 939291 15364 1 148398
6 chr1 924379 926062 1684 * Peak15 Promoter 1 925150 935793 10644 1 148398
transcriptId distanceToTSS ENSEMBL SYMBOL GENENAME
1 ENST00000623808.3 0 ENSG00000228794 LINC01128 long intergenic non-protein coding RNA 1128
2 ENST00000432963.1 0 ENSG00000230368 FAM41C family with sequence similarity 41 member C
3 ENST00000446136.1 0 ENSG00000230368 FAM41C family with sequence similarity 41 member C
4 ENST00000635557.1 0 ENSG00000230368 FAM41C family with sequence similarity 41 member C
5 ENST00000420190.6 0 ENSG00000187634 SAMD11 sterile alpha motif domain containing 11
6 ENST00000437963.5 0 ENSG00000187634 SAMD11 sterile alpha motif domain containing 11
Now if we see first 6 rows we have two genes with three different peaks. When i load and see in the igv browser I do see the there are subtle differences in the accessibility signals.
How to address this issue ,in other words which peak to consider or take all the peak and consider their accessibility as one.
Any suggestion or help would be really appreciated.