Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
HOMER annotation & GO gcorre Bioinformatics 0 12-08-2014 06:47 AM
converting genomic coordinates to transcript coordinates amias Bioinformatics 0 10-25-2014 09:53 PM
Converting mRNA coordinates to chromosome coordinates david.tamborero Bioinformatics 3 10-04-2013 05:46 AM
Indexing in Homer kushald Bioinformatics 0 03-20-2013 09:45 PM
Converting contig coordinates to genomic coordinates aurimas Bioinformatics 0 03-06-2013 11:06 AM

Thread Tools
Old 10-20-2015, 07:57 AM   #1
Junior Member
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: <FILE> hg19 > <OUTPUT_annotated> and works fine.

for custom annotation option, I went to and downloaded canFam3.fa.gz and unzipped the file.

I then did the following: <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.
ajsn6c is offline   Reply With Quote
Old 10-20-2015, 04:09 PM   #2
Senior Member
Location: Montreal

Join Date: May 2013
Posts: 367

Obviously, the FASTA file only contains the chromosome sequences, so you will not obtain any information about the genes if you provide 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.
blancha is offline   Reply With Quote
Old 10-20-2015, 04:12 PM   #3
Junior Member
Location: columbia, missouri

Join Date: Oct 2015
Posts: 7

That makes sense, it talks about adding the GTF file statement at the end. Ill try it out! Thanks!
ajsn6c is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:54 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO