Question: Exon, Intron or Promoter?
0
gravatar for simomll
12 months ago by
simomll0
simomll0 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

ADD COMMENTlink modified 12 months ago by Jennifer Hillman Jackson25k • written 12 months ago by simomll0
1
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink modified 12 months ago • written 12 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour