How do I upload a bigwig file?

Frequently Asked Questions

How can I convert my bam file to a bigwig file, and make it publicly available on JBrowse?


There are at least 4 programs/scripts that are needed to convert a bam to a bigwig file from a standard read mapping bam file. 2 of these are non-standard and will probably need to be downloaded, but are very simple to use and install.

#bioawk can be had from github here  The installation is a breeze: gunzip, cd directory, make.  

#bedGraphToBigWig is part of kents utilities here:

There is not much installation here, but the file does need to be made executable (chmod +x bedGraphToBigWig)


1.  samtools sort example.bam >sorted_example.bam

2.  bedtools genomecov -ibam sorted_example.bam -bga -g genome 738sl.polished.mitoFixed.fa >sorted_example.bdg

3. bioawk -c fastx '{print $name,length($seq)}' genome738sl.polished.mitoFixed.fa >Chr.sizes

4.  bedGraphToBigWig sorted_example.bdg Chr.sizes


No compression or indexing is necessary for a bigwig file, so this file is read to go!

The Jbrowse output looks like this, but changes substantially based on the checking of log scale.