Tag Archives: tdf

Wayback to just-MBD

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.

mbd

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.


In long:
The raw files
raw

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

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

tdf


Rinse and repeat with unmethylated fraction (UNMOTH) and import tdf into IGV!

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