how to analyze gene against peak data in galaxy

Question: how to analyze gene against peak data in galaxy

17 months ago by

mayurdoke • 10 wrote:

I am analysing ChIP-Seq data from Illumina using Galaxy web server. I mapped the reads with bowtie and did the peak calling with Macs. The next thing I wanted to do is to annotate the peaks with genomic regions i.e. promoter, intergenic, intron etc and gene names. I have seen YouTube video where they have shown analysis of genes against peak data in galaxy with the help of RNACHIPintegrator. Now, I tried to search this particular tool in Galaxy cistrome and main galaxy server but could not find it. Can you please help me on this issue. Please find below image showing the genome coordinates.

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chip-seq • 687 views

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modified 17 months ago • written 17 months ago by mayurdoke • 10

17 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The RNACHIPintegrator tool is in the Tool Shed available for use in a local or cloud Galaxy. It may also be hosted at other Public Galaxy servers, but you will need to check the list/instances.

As an alternative, the Deep Tools suite at http://usegalaxy.org contains methods for this type of analysis. See the help section on the tool forms for link outs to usage/example tutorials and a google group where there is active Q&A dedicated to this tools suite and ChIP-seq data analysis.

Or, if you just want to compare overlapping coordinates between two files - one a bed peak file, one an interval/bed file containing regions of interest - tools in the group Operate on Genomic Intervals can be used. BedTools, Compare, Join, and other data manipulation tools are also options. The Galaxy 101 tutorials have some basic examples of how to manipulate data if you are not sure where to start. https://galaxyproject.org/learn/

One last item - double check that format and datatype are assigned correctly for any tool's expected input and make changes as needed. https://galaxyproject.org/support/

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 17 months ago • written 17 months ago by Jennifer Hillman Jackson ♦ 25k

17 months ago by

mayurdoke • 10

mayurdoke • 10 wrote:

Hello,

As per your suggestion, I am going to install Galaxy local and RNACHIPintegrator tool on my computer. Will be the display or interface of a local galaxy as same as Public galaxy server? I have another question regarding gene expression. How can I determine the up and down regulation of genes from Chip-seq data?

ADD COMMENT • link written 17 months ago by mayurdoke • 10

Please see the latest tutorials here: https://galaxyproject.org/learn/

ADD REPLY • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k

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