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Old 10-20-2015, 07:57 AM   #1
ajsn6c
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Location: columbia, missouri

Join Date: Oct 2015
Posts: 7
Default Annotating dog coordinates using HOMER

So I have a bed file with dog genomic coordinates e.g. chr38 1232122 123555

I would like to use HOMER to annotate this. I use HOMER to annotate human peaks using the command:

annotatePeaks.pl <FILE> hg19 > <OUTPUT_annotated> and works fine.

for custom annotation option, I went to http://hgdownload.soe.ucsc.edu/golde...nFam3/bigZips/ and downloaded canFam3.fa.gz and unzipped the file.

I then did the following: annotatePeaks.pl <FILE> canFam.fa > <OUTPUT_annotated>

This was the output:

Skipping TSS assignment (can't find file for genome canFam3.fa)
Can't find promoterFile canFam3.fa/canFam3.fa.tss
Could not find basic annotation file (canFam3.fa/canFam3.fa.annotation)
Could not find full/detailed annotation file (canFam3.fa/canFam3.fa.annotation)
Counting Tags in Peaks from each directory...
Organism: unknown

Its not giving me the genes associated with the peaks, am I downloading the right file (canFam3.fa)? canFam3.fa is in the same directory as my bed file, so it should be finding it, if it is. What would you recommend me doing?

P.S. Not that bioinformatically skilled, but willing to learn.
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Old 10-20-2015, 04:09 PM   #2
blancha
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Location: Montreal

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Default

Obviously, the FASTA file only contains the chromosome sequences, so you will not obtain any information about the genes if you provide annotatePeaks.pl only with the FASTA file.

You also want to provide HOMER with the annotation information, contained in a GTF file, using the argument --gtf.

You can download the GTF file from the UCSC Table Browser.
I prefer Ensembl, but the GTF file from Ensembl may use a different nomenclature for the chromosomes. If using the GTF file from Ensembl, you'll have to check the nomenclature in your BED file and change it, if necessary.
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Old 10-20-2015, 04:12 PM   #3
ajsn6c
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Location: columbia, missouri

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Default

That makes sense, it talks about adding the GTF file statement at the end. Ill try it out! Thanks!
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