Converting Coordinates Of Peak File From Hg18 To Hg19

Question

[Dataminer]

Hi!

I have a peak file generated using MACS and human genome18, what I want is to convert/update the coordinates of this file to human genome 19.

Any suggestions, as how to deal with this situation?

Thank you

Answer 1

[brentp]

Use LiftOver from UCSC. You'll need a chain file and the downloadable executable from here: http://hgdownload.cse.ucsc.edu/admin/exe/ Otherwise, you can use the web interface.

[Dataminer]

@Brent: Thank you. One last question is their an automated way/webserver to annotate these peaks in a window of 25kb to a single nearest gene.

[brentp]

search biostars for annotating with biomaRt, e.g.: http://www.biostars.org/post/show/2936/default-upstream_flank-value-used-in-getbm-in-biomart/ but there are others as well.