annotatePeaks.pl Homer using "RNA"

Question

[reubenmcgregor88]

Hi all, I have successfully used the following function in Homer to annotate my peaks to closest genes:

annotatePeaks.pl <peak/BED file> <genome>   > <output file>

i.e. annotatePeaks.pl ERpeaks.txt hg18   > outputfile.txt

My problem is that some of my peaks are in the middle of introns of genes but are being called to the next gene as the tss of that gene is closer to the centre of the peak. Whether this is "right" or "wrong is a matter for debate, but what I would like to do is annotate peaks to closest RNA, the manual says the following on the matter

Peak vs. tss/tts/rna mode (works with custom GTF file): If the first argument is "tss" (i.e. annotatePeaks.pl tss hg18 ...) then a TSS centric analysis will be carried out. Tag counts and motifs will be found relative to the TSS. (no position file needed) ["tts" now works too - e.g. 3' end of gene] ["rna" specifies gene bodies, will automaticall set "-size given"]

So in theory if I used the following command:

annotatePeaks.pl rna ERpeaks.txt hg18 etc

It should work, but this brings back errors saying "rna" is not allowed in the line.

Any ideas how this can be achieved?

Answer 1

[CrisMar]

Maybe this might help you: Annotating bed files with Crosslinking induced truncations sites from iCLIP experiment (chromosome locations).

Answer 2

[Joseph Hughes]

I think you need to use -rna, it looks like you are forgetting the hyphen.

From the website:

Search for RNA motifs ("-rna")

If looking at RNA data (i.e. Clip-Seq or similar), this option will restrict HOMER to only search the + strand (relative to the peak), and will output RNA motif logos (i.e. U instead of T). It will also try to compare found motifs to an RNA motif database, which sadly, only contains miRNAs right now... I guess chuck roundhouse kicked all of the splicing and other RNA motifs into hard to find databases.

[reubenmcgregor88]

Sorry I meant to ask about annotatePeaks.pl not the motif searching, I have updated the post