Hello,

There is no general workflow, primarily because there is no single source of gene annotation and some formatting may be necessary. But once that part is resolved, using a single tool in "Operate on Genomic Intervals" can most often assign gene names to query genome regions.


The first step is to obtain a dataset that has gene names assigned to genome regions. This data should be based on the same reference genome as your peak intervals.

Sources can vary by species and reference genome build. For most model organisms, a source can be found in the set of linked projects under "Get Data" and the dataset directly imported into Galaxy. For certain genomes at UCSC, the tool "Operate on Genomic Intervals -> Profile Annotations" is a quick way to see which UCSC Gene tracks are associated. The RefSeq Genes track would be one example.

Once in Galaxy, use the tools in "Operate on Genomic Intervals" to compare your peak intervals with gene intervals and link in gene names. "Join" would be the simplest option. Help is located on each tool's form, including links to the wiki and screencasts, but also directly here:
http://galaxyproject.org/wiki/Learn/Interval%20Operations

Hopefully this helps,

Best,

Jen
Galaxy team

On 12/6/11 9:31 AM, Dr Chris Futtner, Ph.D. wrote:
Can anyone point me to a good workflow to convert my ChIP-seq data
intervals to gene names. My peaks fall both within genes and within
intergenic areas.
Thanks,
Chris

Christopher Futtner, Ph.D.
Dept. of Surgery
Duke University
Durham, NC 27710
email: christopher.futt...@duke.edu
phone: 919-684-1183


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