BigWig file tracks are blank

[eliza-naismith]

Hi, I have BigWig files (converted from .wig files) containing the positions of Tn-seq insertions. The files are stored locally on my computer, and I upload them within the desktop app using the 'open tracks' and BigWig adaptor > Quantitative track. However each time I try to upload these into JBrowse the tracks are blank, even though the y-axis has the correct min/max range. Am I doing something wrong?

[cmdcolin]

The most common cause of a track being blank is for the "refseq" names to mismatch e.g. the FASTA file says chr1 but the data file says e.g. chrom1. You can use the command "bigWigInfo -chroms volvox-sorted.bam.coverage.bw" using the bigWigInfo command from UCSC (or you can look at your plaintext wig file for the same thing, just search the wig for e.g. LT708304.1)

Random extra note: we're considering adding a built in tool for doing this as well so that you can verify this in the app!

[cmdcolin]

Extra extra note: if you can see that the refnames look correct in the file, but you're still not seeing data, that would probably be a weird bug. I'd be interested to see the bigwig file in that case

[eliza-naismith]

Thank you for your prompt reply, so helpful as I'm new to using JBrowse! I took a closer look at the refseq names in my original FASTA file and had made an error when generating the bigWig file - the track is working now perfectly. I do like the sound of the built in tool for verifying the names in the app. 😄