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