Homer with custom genome

Question

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I am trying to annotate peaks identified uisng MACS14 , using homer annotatePeaks.pl option but the organism is not listed in the homer ,so I am trying to add new organism using loadGenomes.ploption of homer which required gtf file but Iam unable to add it , can any one tell me how to fix it , I am using following command :

perl /homer.v4.8.3/.//configureHomer.pl -install custom_organism.gtf

Also if there is/are any other tool/s for annotating peaks will be helpful.

Thanks in advance

Answer 1

[ejm32]

According to homer docs you should load the genome as follows:

loadGenome.pl -name custom_organism -org null -fasta custom_organism.fa -gtf custom_organism.gtf

Also, you can annotate without "installing" the genome into homer.

annotatePeaks.pl peak_pos.bed custom_organism.fa -gtf custom_organism.gtf > output.txt

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thanks I have installed the genome.

1.After that I have run following command for annotating : (cmd=annotatePeaks.pl peak.txt genome -gtf *.gtf) output contains following columns :

PeakID Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type

But the columns from EntrezId to Genetype is empty

1. Secondly, I am trying to view these peaks but mostly all the tools are for model organisms any idea for that?

[ejm32]

1. For viewing I would look in the Integrated Genome Viewer (IGV) from Broad, you can load gtfs and coverage and beds into a session.

2. As for the missing column data, that may be because your GTF's ids do not map to EntrezIDs. I would also check to make sure that the gtf and peak file have the same chromosome name format. without seeing any data there's not much else I can thing of.

good luck!

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Thanks for your answer its really helpful i could view results in IGV.

My next query is regarding how to you interpret the results , presence of peaks and/or absence of peaks on same gene but different sample ?

[ejm32]

Can you be more specific? Understanding ChIP-seq data is the focus of many lab's primary research...

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I am working on ATAC seq

[ejm32]

I meant, you need to describe the question you are trying to ask and your experimental setup.

[ejm32]

I meant, you need to describe the question you are trying to ask and your experimental setup.