bedgraph-to-bigwig error

usegalaxy.eu support
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tool: bedgraph-to-bigwig

input: bedgraph files from MACS2 output

problem: result bigwig file has 0 lines

tool standard output: hashMustFindVal: ‘GL456210.1’ not found
tool standard error" grep: write error: Broken pipe Error running wigToBigWig.

more details: I used mm39 as the database/build for all my inputs, and I can see lines with GL456210.1 in the first column of the bedgraph file.

I want to use the resulting bigwig for computematrix. I’ve also tried to directly run computematrix on the bedgraphs but run into error presumably due to the same problem. Please help!

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Welcome, @Adrian1

The tool is comparing the term in your file to the reference genome. If you are working at UseGalaxy.org, then mm39 would be a custom reference genome. Check the format of that fasta, and the custom “database” you created for it. Is the key unique, and it is assigned to your input data?

Help → Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at

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Thank you for your response. I know that usegalaxy.org has no mm39, but I’ve read the usegalaxy.eu does have, so I’ve been using usegalaxy.eu

I can try the solution you mentioned, but I’m wondering if there is known problems about missing data in the mm39 genome in usegalaxy.eu? Would you happen to know how I can access the mm39 genome in usegalaxy.eu to dig into its annotation/sequence to find if those values are missing?

Thank you

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The version of mm39 indexed at UseGalaxy.eu is sourced from UCSC here UCSC Genome Browser Downloads

FAQ: Mismatched Chromosome identifiers and how to avoid them → Directly obtaining UCSC sourced *genome* identifiers

This is a history with the identifiers extracted. The name is slightly different as chr1_GL456210v1_random. Galaxy | Europe

To convert identifiers, this tool can be used → Replace column by values which are defined in a convert file

Scroll down to the bottom on the tool form to the help section find the link out to a repository with common mapping files.

This tutorial has more manipulations, should you need to construct your own mapping file. Data Manipulation Olympics

Hope this helps!