Prior to bisulfite sequencing we did do a couple of MBD enrichment libraries to describe DNA methylation in oysters. Results even were snuck into this perspective.
While I am sure there are genome tracks around, I am ending up #doingitagain.
In short I took the raw Solid reads, align to
Crassostrea_gigas.GCA_000297895.1.26.dna.genome in CLC, exported bam, converted to bedgraph, converted to tdf.
The raw files
1) Imported into CLC v8.0.1
Discard read names = Yes Discard quality scores = No Original resource = /Users/sr320/data-genomic/tentacle/solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_SB_METH/solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_QV_SB_MOTH.qual Original resource = /Users/sr320/data-genomic/tentacle/solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_SB_METH/solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_SB_MOTH.csfasta
(yes the core called them MOTH)
2) Reads were mapped
3) Exported as BAM.
4) Converted to bedgraph
!/Applications/bioinfo/bedtools2/bin/genomeCoverageBed -bg -ibam /Users/sr320/data-genomic/tentacle/solid0078_moth.bam -g /Volumes/web/halfshell/qdod3/Cg.GCA_000297895.1.25.dna_sm.toplevel.genome > /Users/sr320/data-genomic/tentacle/MBD-meth.bedgraph
5) Converted to toTDF
Rinse and repeat with unmethylated fraction (UNMOTH) and import tdf into IGV!