Aligning Chip-Seq Reads To Custom Tss Files Using Homer

Question

[bede.portz]

Hello,

I am attempting to align ChIP-seq reads to a custom TSS file using annotatePeaks in HOMER, but I can't figure out how to do this. It should be possible, using -cTSS, However I can't seem to figure out the correct usage from the documentation or extensive trial and error. My custom TSS file is a .bed. Is this an acceptable file format?

Any help would be appreciated.

Bede

Answer 1

[bede.portz]

This question got a lot of views but no answer. Below is the solution I found. One can simply use any TSS file (or any reference file for that matter) as a HOMER peaks file or .bed file, as the peaks file against which your reads/peaks of interest will be mapped, and just ignore the tss function of HOMER entirely.

$annotatePeaks <custom_tss.bed> <genome> -d <tag directory containing reads> -options > output.txt

in this example the customer tss file was a .bed and the ChIP-seq reads were in a tag directory made by HOMER using makeTagDirectory and the genome is the genome as downloaded via HOMER.