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Question: Looking for Dnase-seq analysis workflow
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gravatar for rijnkel
4.3 years ago by
rijnkel • 0
United States
rijnkel • 0 wrote:

Does any one have a workflow to analyze Dnase-seq data?(from fastq to "peaks") and are willing to share

thanks Monique
dnase-seq alignment • 928 views
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modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by rijnkel • 0
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gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi Monique,

I don't have one specifically to share, so others are still welcome to post, but I can provide some general information about how to proceed.

Reviewing the methods used in ENCODE projects at the UCSC Genome Browser (http://genome.ucsc.edu -> ENCODE) will give you an overview of common tools involved. Then you can set up a production local or cloud Galaxy, and use the same or analogous tools as available. Check the Tool Shed for options. You want to do some basic QC, map, then do the peak calling in the same order as for other similar expression analysis, so any of those resources/tutorials that are shared on the Main server or in our Wiki would be also worth reviewing.

Some Galaxy links:
http://usegalaxy.org/cloud
http://usegalaxy.org/toolshed
http://galaxyproject.org -> Learn

I also did a quick search using the keywords "DNase" and "Galaxy" and some potentially interesting links came up. 

Best, Jen, Galaxy team
ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
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