Although I found that the chromStart positions in HOMER output have a +1 shift compare to other software, I did not realize this issue since all other software are consistent.
Until recently, I found BAM, BCF, BED and PSL formats are using the 0-based coordinate system, while SAM, VCF, GFF and Wiggle formats are using the 1-based coordinate system.
For BED file format, we can refer to http://asia.ensembl.org/info/website/upload/bed.html.
In addition, the 0-based coordinate system is specified by a half-closed-half-open interval. For example, the first 100 bases of a chromosome are defined as [0, 100), that span the bases numbered 0-99. While the 1-based coordinate system is specified by a closed interval, for example the above region is [1, 100].
Most of the software for ChIP annotation doesn’t considered this issue when annotating peak (0-based) to transcript (1-based). To my knowledge, only HOMER consider this issue. After I figure this out, I have updated ChIPseeker (version >= 1.4.3) to fix the issue.
Please bare in mind that chromStart in ChIPseeker has +1bp shift compare to the number recorded in BED file.