[BioC] iSeq Peak Position

Dario Strbenac D.Strbenac at garvan.org.au
Thu May 17 06:00:11 CEST 2012


I think the suggestion in the vignette is misleading.

"To infer the actual binding sites, one may add 13 bp to the peak position because the tags' length is 25 bp. If the middle positions of the sequence tags are used as the genomic positions, the user doesn't need to do the adjustment."

I think it is important to remember that even though the tag is 25bp, the DNA fragment is typically bigger, around 300 bp. The position of a ChIP peak then is not the middle position of a tag. Also, it's worth noting that by the definition used by iSeq, the positions of the ChIP peaks can change simply by having a dataset with a longer read length, or a different end clipping scheme, even if all of the tags start in the same location.

Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010

More information about the Bioconductor mailing list