Homer detailed annotation

Question

[xiaofeiwang198266]

Dear,

I used HOMER annotatePeaks.pl to annotate my peaks.

Here is the format for my code:

annotatePeaks.pl peak.bed ref.fa -gff3 ref.gff3 > PeakAnno.txt.

But, I don't know why it is "NA" for the columns of "Focus Ratio/Region Size" and Detailed Annotation""? I am more interested in the "Detailed Annotation".

Really hope I can get it fixed here. Is it the problem with my code or my annotation file? I did not get answer from the manual http://homer.ucsd.edu/homer/ngs/annotation.html and any threads neither.

Thank you so much!

Best,

X

[Lila M]

Are you using a genome included in homer software?

[GenoMax]

Please use ADD COMMENT/ADD REPLY when asking clarifications about existing posts to keep threads logically organized.

[xiaofeiwang198266]

No, not included in homer, that is why I gave the .fa and .gff3. The detailed annotation only works out for included genome? But, I believe there are repeats information in my .gff3. I will double check this, thought.

X

Answer 1

[Lila M]

So you should load the genome first, try this:

loadGenome.pl -name name_organism -org organism -fasta organism.fa -gff3 organism.gtf

annotatePeaks.pl file.bed organism.fa -gff3 organism.gtf > output.txt

It should work

[xiaofeiwang198266]

Got it, thanks a lot! X

[GenoMax]

Great! If this fixes the problem then you can "move" this post to an answer, once you hear from xiaofeiwang198266

[xiaofeiwang198266]

I will try and let people know.

[xiaofeiwang198266]

Could I ask another question? It is about pos2bed.pl not associated with this one. Or, do I need to open another thread?

[GenoMax]

If it is a different question open a new thread.

[xiaofeiwang198266]

I tired this

but got this

"Could not find full/detailed annotation file (~/software/homer/.//data/genomes/sorgBi1.31//sorgBi1.31.annotation)"

I think I need this detailed annotation filed created when use loadGenome.pl, but don't know how or why it is not generated when using loadGenome.pl.

[Lila M]

Which genome and organism are you using?

[xiaofeiwang198266]

Sorghum bicolor. Does is matter for this? On my understanding, "loadGenome.pl" is to prepare a custom genome for use with HOMER, so I don't think it will pull any information from Homer?

[xiaofeiwang198266]

Also, I downloaded hg18 genome to see the difference with my custom genome. There are lots of information under ~/software/homer/data/genome/hg18:

chrom.sizes hg18.rna hg18.tts hg18.tss hg18.stop hg18.splice5p hg18.splice3p hg18.miRNA hg18.aug hg18.repeats hg18.basic.annotation hg18.full.annotation

and ect.

But, there are only

sorgBi1.31.rna sorgBi1.31.tss sorgBi1.31.tts sorgBi1.31.basic.annotation

here under ~/software/homer/data/genomes/sorgBi1.31.

So, I think there should some way I can generate the other information, including *.full.annotation, right?

[yeji]

were you able to fix this problem?

[Bryan]

Hi Lila,

I installed homer and want to annotate my peaks using the mm10 genome. The genome is already installed and I can get the normal output. But the "detailed annotation" column is NA. Do you know how to fix it? Thank you a lot!

Bryan