Tag Archives: visualization

First steps at an aggregated view of all DNA methylation data (updated)

Seems like I have gotten close (see here) but do not have a canonical IGV session that has all of our DNA methylation data. The goal here is to generate such a product (and publish, so I do not lose it).

All data is publicly available at


see also data on Figshare


July 2, 2015 – added Heat Shock experiment alternative splice track
June 26, 2015 – add link to Figshare version
June 26, 2015 – updated Archive.zip
June 26, 2015 – added numerous array tracks from heat stress array experiment including 3+ tracks.
June 26, 2015 – added new track from heat stress – Heat-multi-individual-dmr.bed
June 22, 2015 – updated Archive.zip
June 22, 2015 – updated MBD-seq track gills (no bisulfite treatment) to use unique mapping (see also [this](MBD-seq track gills (no bisulfite treatment))
June 22, 2015 – Updated EE2 linkout to go to Github
June 22, 2015 – Corrected error in labelling EE2 experiment tracks
June 15, 2015 – added MBD-seq track gills (no bisulfite treatment)
June 15, 2015 – added larval pesticide treatment tracks (bisulfite treatment)
June 15, 2015 – new IGV screenshot
June 15, 2015 – added HS-Cuffdiff_geneexp.sig.gtf (differentially expressed genes from heat-shock)




FileID Description Links
Crassostrea_gigas.GCA_000297895.1.26.gtf gtf ftp
MBD-Gill-meth MBD enriched DNA library alignment paper, info
BiGill_CpG_methylation gill methylation 5x (MBD-BS, hi output) paper
BiGill_exon_clc_rpkm Corresponding exon-specific gene expression paper
BiGo_CpG_methylation male gamete methylation 5x (hi output) paper
M1 male gamete methylation 5x preprint
M3 male gamete methylation 5x preprint
T1D3 72hpf larvae from M1 methylation 5x preprint
T1D5 120hpf larvae from M1 methylation 5x preprint
T3D3 72hpf larvae from M3 methylation 5x preprint
T3D5 120hpf larvae from M3 methylation 5x preprint
Heat-multi-individual-dmr.bed Heat Stress (13 locations) common signal notebook
2M_3plusmerge_Hyper.bed merging adj probes to single interval notebook
2M_3plusmerge_Hypo.bed merging adj probes to single interval notebook
4M_3plusmerge_Hyper.bed merging adj probes to single interval notebook
4M_3plusmerge_Hypo.bed merging adj probes to single interval notebook
6M_3plusmerge_Hyper.bed merging adj probes to single interval notebook
6M_3plusmerge_Hypo.bed merging adj probes to single interval notebook
2M_Hyper_3plusAdjactentProbes.gff 3+ adjacent probes notebook
2M_Hypo_3plusAdjactentProbes.gff 3+ adjacent probes notebook
4M_Hyper_3plusAdjactentProbes.gff 3+ adjacent probes notebook
4M_Hypo_3plusAdjactentProbes.gff 3+ adjacent probes notebook
6M_Hyper_3plusAdjactentProbes.gff 3+ adjacent probes notebook
6M_Hypo_3plusAdjactentProbes.gff 3+ adjacent probes notebook
2M_sig Heat stress DMRs (array), ind.#2 notebook, draft
4M_sig Heat stress DMRs (array), ind.#4 notebook, draft
6M_sig Heat stress DMRs (array), ind.#6 notebook, draft
HS-Cuffdiff_geneexp.sig.gtf Heat stress differentially expressed genes notebook
HS-Cuffdiff_altsplice.bed Heat stress alternatively spliced genes notebook
2M.bedgraph.tdf RNA-seq from ind.#2 above – pretreament notebook, draft
4M.bedgraph.tdf RNA-seq from ind.#4 above – pretreament notebook, draft
6M.bedgraph.tdf RNA-seq from ind.#6 above – pretreament notebook, draft
2M-HS.bedgraph.tdf RNA-seq from ind.#2 above – post-heatshock notebook, draft
4M-HS.bedgraph.tdf RNA-seq from ind.#4 above – post-heatshock notebook, draft
6M-HS.bedgraph.tdf RNA-seq from ind.#6 above – post-heatshock notebook, draft
mgaveryDMRs_112212.gff EE2 exposure DMRs (array) paper
A01.smoothed EE2 exposure array data – input versus input paper
A02.smoothed EE2 exposure array data – EE2 vs control paper
A03.smoothed EE2 exposure array data – EE2 vs control (dyeswap) paper
YE_mixHYPER.bed DMRs in pesticide exposed larvae (hypermethylated)
YE_mixHYPO.bed DMRs in pesticide exposed larvae (hypomethylated)
YE_mix_22smCG3x larvae (mix pesticide exposed) methylation
YE_control_22smCG3x larvae (control) methylation


anyone should be able to render this in IGV with this session file:


This work was supported in part by the National Science Foundation (NSF) under Grant Number 1158119 awarded to SR Roberts


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.


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

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

-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!