bedgraph-to-bigwig error

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!

Welcome, @Adrian1

The tool is comparing the term in your file to the reference genome. If you are working at, 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

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

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

Thank you

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

FAQ: Mismatched Chromosome identifiers and how to avoid themDirectly 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!