DML Analysis Part 41
One last set of analyses before dedicated writing
Special Issue deadline: Oct. 1 Today: Sept. 26 Hours to get this wrapped up: at least 56
I told myself that after today, I would focus solely on fishing up the draft paper text before going down the rabbit hole of refining figures and cleaning up analyses. Here’s what I got done today:
Fixing the promoter track
During the last E2O meeting, I was tasked with checking that the promoter track I used accounted for mRNA directionality. I loaded my upstream flank track and mRNA track into IGV to check.
Figure 1. IGV screenshot with upstream flanks (promoter track) and mRNA confirming how I forked up.
In this notebook, I went to correct my promoter track. I started with the 1000 bp upstream and downstream flanks I already created for each mRNA transcript. Looking at the tracks, I remebered that there was a strand indication! Some transcripts are on the forward strand (+) while others are on the reverse strand (-). To fix the promoter track, I needed the upstream flank information to only include forward strand transcripts, and the downstream flanks should only include reverse strands. I used
grep to get this done:
!grep ". + ." 2019-05-29-Flanking-Analysis/2019-05-29-mRNA-Upstream-Flanks.bed \ > 2019-05-29-Flanking-Analysis/2019-05-29-mRNA-Upstream-Flanks-Forward-Strands.bed !grep ". - ." 2019-05-29-Flanking-Analysis/2019-05-29-mRNA-Downstream-Flanks.bed \ > 2019-05-29-Flanking-Analysis/2019-05-29-mRNA-Downstream-Flanks-Reverse-Strands.bed
I then combined the individual tracks using
!cat \ 2019-05-29-Flanking-Analysis/2019-05-29-mRNA-Upstream-Flanks-Forward-Strands.bed \ 2019-05-29-Flanking-Analysis/2019-05-29-mRNA-Downstream-Flanks-Reverse-Strands.bed \ > 2019-05-29-Flanking-Analysis/2019-05-29-mRNA-Promoter-Track.bed
With the new promoter track, I recharacterized overlaps between various genomic features and DML. There were some changes to the number of overlaps, but it didn’t change the overall pattern. Time to write!
- Update methods and results
- Update paper repository
- Outline the discussion
- Write the discussion
- Write the introduction
- Revise my abstract
- Share the draft with collaborators and get feedback
- Post the paper on bioRXiv
- Submit to the Special Issue