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Question: Exon, Intron or Promoter?
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gravatar for simomll
12 months ago by
simomll • 0
simomll • 0 wrote:

Hello, I need help you. I have a file of CHIP-SEQ data in BED format and i analyzed those data with IGV ("manually") and with Galaxy at the same time, resulting in a list of genes corresponding to my peaks.

Now, I would obtain more information: I would know if the peaks on my file.bed interest the exon, intron or promoter region of the corresponding gene and I would do it with galaxy.

I hope to explain well my question. How can I do it?

Thank you.

Simone

promoter bed interval intersect chip-seq • 624 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by simomll • 0
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Any BED or interval dataset can be compared with another to find common regions of overlap if the coordinates are based on the same reference genome.

UCSC can be a good source for reference annotation in BED format. If you have gene names/symbols those can be used as filtering criteria when extracting data from a track. Or you can select all of the promoter, exon, intron (and other features, as available) for all genes/transcripts in a track and compare from there, link in identifiers (gene names), and perform downstream analysis/graphing.

Several Galaxy tutorials cover methods to do this type of analysis: https://galaxyproject.org/learn/

Start here with the 101, which shows the simplest way to directly compare two bed/interval datasets to find common regions:

Then see:

I also updated the tags in this post. If you look at the right sidebar now, you will find other similar Q&A that may be helpful. >>>

Hope that helps! Jen, Galaxy team
ADD COMMENT • link modified 12 months ago • written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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