How do I upload a bigwig file?

There are at least four programs/scripts that are needed to convert a bam to a bigwig 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. 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.

Screenshot of Jbrowse output