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 here https://github.com/lh3/bioawk. The installation is a breeze: gunzip, cd directory, make.
#bedGraphToBigWig is part of kents utilities here: https://github.com/ENCODE-DCC/kentUtils/blob/master/src/utils/bedGraphTo....
There is not much installation here, but the file does need to be made executable (chmod +x bedGraphToBigWig)
- samtools sort example.bam >sorted_example.bam
- bedtools genomecov -ibam sorted_example.bam -bga -g genome 738sl.polished.mitoFixed.fa >sorted_example.bdg
- bioawk -c fastx '{print $name,length($seq)}' genome738sl.polished.mitoFixed.fa >Chr.sizes
- bedGraphToBigWig sorted_example.bdg Chr.sizes sorted_example.bw
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.
