Check gene.gff has 63227 genes

[hputnam]

there are genes with names starting with g and with adig, need to check we pulled them all

[yaaminiv]

Will include GeMoMa genes/CDS/introns etc. in Mcap tracks

[yaaminiv]

Remade genome feature tracks. Gene track now has 63227 genes

gene: https://github.com/hputnam/Meth_Compare/blob/master/genome-feature-files/Mcap.GFFannotation.gene.gff CDS: https://github.com/hputnam/Meth_Compare/blob/master/genome-feature-files/Mcap.GFFannotation.CDS.gff intron: https://github.com/hputnam/Meth_Compare/blob/master/genome-feature-files/Mcap.GFFannotation.intron.gff upstream flanks: https://github.com/hputnam/Meth_Compare/blob/master/genome-feature-files/Mcap.GFFannotation.flanks.Upstream.gff downstream flanks: https://github.com/hputnam/Meth_Compare/blob/master/genome-feature-files/Mcap.GFFannotation.flanks.Downstream.gff intergenic: https://github.com/hputnam/Meth_Compare/blob/master/genome-feature-files/Mcap.GFFannotation.intergenic.bed

Also remade Mcap figure based on overlaps with additional GeMoMa/adig genes. MBD is no longer the best.

[hputnam]

wrote a script to fix the Mcap gff file to correct formatting of GeMoMa genes https://github.com/hputnam/Meth_Compare/blob/master/scripts/Fix_GeMoMa.R