Posted by & filed under Cgigas DNA Methylation.

Having just given a talk on reproducibility, I am in the midst of responding to reviewer comments about what we did (12 months ago!) and boy can I say every minute of putting this notebook together was worth it. I even found where we ran the entire notebook, so all result files are easily accessible. Beyond praising Claire, I will document my follow up analysis here.

Essentially the want more quantitative information on differential methylation beyond ..

OlsonandRoberts2015_9_docx_1BC2FBAE.png

Makes sense.

Here is what was originally done.

olson-ms-nb_BiGo_dev_ipynb_at_master_·_che625_olson-ms-nb_1BC2FCC5.png

For example the file named linexon contained 16 exon_intersect_DML_lin_u.txt. The 4 files were concatenated to produce lintable ….

eagle_fish_washington_edu_cnidarian_olson-ms-nb-master_12_1714_wd_lintable_1BC2FE30.png

and a little awk

awk 'FNR==NR{sum+=$1;next}; {print $0,sum}' lintable{,} > lin_total
awk '{print $2, $1, $3, (($1/$3)*100)}' lin_total > lineage_DMLs

to create lineage_DMLs

eagle_fish_washington_edu_cnidarian_olson-ms-nb-master_12_1714_wd_lineage_DMLs_1BC2FE65.png


Analogously here are the developmental_DMLs….

eagle_fish_washington_edu_cnidarian_olson-ms-nb-master_12_1714_wd_developmental_DMLs_1BC3F775.png


And we certainly need to now how many all_CGs we have…

eagle_fish_washington_edu_cnidarian_olson-ms-nb-master_12_1714_wd_all_CGs_1BC3F807.png


Table

Feature Family specific DMLs Developmental specific DMLs
Transposable Element 17 16
Promoter Region 2 3
Exon 16 12
Intron 25 46

I know we did this before, but I believe the reviewers want a break-down, or list of which specific transposable elements. This is a long shot if I can find this…
2 minutes later https://github.com/sr320/ipython_nb/blob/master/BiGo_larvae_manuscript4.ipynb.


To be sure files are accurate, I will intersectbed again. Based on recollection there is likely not a difference in proportion based on all TEs. This brings up a an important point of how to record “negative” data that does not go into a paper.

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