parsing BED coordinates

[This article was first published on YGC » R, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

In supplemental file of ChIPseeker paper. I compare distances to TSS reported by several ChIP annotation software, including ChIPseeker, ChIPpeakAnno, HOMER and PeakAnalyzer.

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.

Related Posts

To leave a comment for the author, please follow the link and comment on their blog: YGC » R.

R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)