Need help with "Create a BedGraph of genome coverage" tool

Question: Need help with "Create a BedGraph of genome coverage" tool

4.3 years ago by

Hi there

I am trying to calculate the coverage of my alignment based on the BAM file using "Create a BedGraph of genome coverage". I have converted the SAM file to BAM file and I am using a custom-build genome, which I have imported into Galaxy as a fasta file. When running the Bedgraph command I get the message "Unspecified genome build, click the pencil icon in the history item to set the genome build". Should I press the pencil icon on the BAM file of interest - and if I do so, how to tell the program that it should use my custom-build genome? The genome (as FASTA) is already imported to the history of use. How to make it able for me to use the genome of interest which is not a default in the program?

I am stucked here, so please help me :-)

Tool name: Create a BedGraph of genome coverage
Tool version: 0.1.0
Tool ID: toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_genomecoveragebed_bedgraph/0.1.0
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/aaronquinlan/bedtools

create-a-bedgraph-of-genome-coverage • 1.8k views

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modified 4.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by christensentrine • 10

4.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

To perform this operation, create a "Custom Build" from your custom genome's fasta dataset. Do this under 'User -> Custom Builds'. Once created, you will be able to assign the 'database' attribute just like any other reference genome that is native (already cashed on the instance). In short, click on the pencil icon for a dataset that you want to assign the build to and on the first tab, all of your Custom Builds will appear in the Reference Genome pull-down menu. Select the proper one and save.

This is useful for certain tools that require 'database' assigned (such as this one) and in particular when using Trackster ("Visualization") with a custom reference genome.

Hope this helps! Jen, Galaxy team

ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

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