I am working with some BS methylation data in BedGraph form. Here is what the data looks like:
genome 168326 168326 1
genome 168407 168407 1
genome 168408 168408 3
genome 168420 168420 1
genome 168421 168421 2
genome 168449 168449 5
genome 168450 168450 1
Obviously the genome is the actual name, but anyways. I am having trouble converting it into a UCSC binary data format for loading into a track hub. I have kent tools installed and have tried running bedGraphToBigWig on the the files, which completes without error. When I load the bigWig files the tracks are blank. I did some further investigation by running the bigWigs through bigWigToBedGraph, which again completed without error but returned an empty file. I tried converting the bigWigs to wigs using bigWigToWig and got the following output:
#bedGraph section genome:165-55617
#bedGraph section genome:55626-72139
#bedGraph section genome:72140-102836
#bedGraph section genome:102837-136403
#bedGraph section genome:136426-166013
#bedGraph section genome:166014-172052
If I upload the tracks as custom tracks in bedGraph format they display fine. I made sure they were sorted and ran them through bedGraphPack and nothing changed.
Has anyone encountered this before?
BedGraph is 0-based half open, so you're specifying 0-width entries. I imagine that that could cause many problems.
Do you have a few example lines from your file? Or a link to your bigWig file?
The top red code block is an example of the bedGraph file I am working with, and the bottom block is what the wig file looks like when I convert bedGraph -> bigWig -> wig.
If I convert bedGraph -> bigWig -> bedGraph I get an empty file.
As for the bigWig I don't imagine you'd like to see a few lines of that :)
Can you specify a few real lines, not mock-up lines? Can you also tell us which genome you are using?
Here are some real lines:
The genome is one we 'created', which is an EBV virus genome with a GFP insert. We have a custom deployment of the UCSC browser. I have set up and viewed many things with this genome on custom track hubs so I am confident that the issue is with these files.
Your features have all 0-length. What is this supposed to show? Do you mean 1-bp long features?
What does your chrom.sizes file look like? I am not sure if underscores are legal in chromosome names in UCSC.
Here is the output of
bigWigInfo
on the bigWig file:Seems like the bigWig is clearly messed up!