Question: Homer detailed annotation
1
gravatar for xiaofeiwang198266
2.2 years ago by
United States
xiaofeiwang19826620 wrote:

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

annotate peaks chip-seq homer • 1.7k views
ADD COMMENTlink modified 2.2 years ago by Lila M 470 • written 2.2 years ago by xiaofeiwang19826620

Are you using a genome included in homer software?

ADD REPLYlink written 2.2 years ago by Lila M 470
1

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

ADD REPLYlink written 2.2 years ago by genomax67k

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by xiaofeiwang19826620
0
gravatar for Lila M
2.2 years ago by
Lila M 470
UK
Lila M 470 wrote:

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

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Lila M 470
1

Got it, thanks a lot! X

ADD REPLYlink written 2.2 years ago by xiaofeiwang19826620

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

ADD REPLYlink written 2.2 years ago by genomax67k

I will try and let people know.

ADD REPLYlink written 2.2 years ago by xiaofeiwang19826620

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

ADD REPLYlink written 2.2 years ago by xiaofeiwang19826620

If it is a different question open a new thread.

ADD REPLYlink written 2.2 years ago by genomax67k

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.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by xiaofeiwang19826620

Which genome and organism are you using?

ADD REPLYlink written 2.2 years ago by Lila M 470

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?

ADD REPLYlink written 2.2 years ago by xiaofeiwang19826620

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?

ADD REPLYlink written 2.2 years ago by xiaofeiwang19826620
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