Separate upstream and downstream flanks

[yaaminiv]

In this notebook, I'm trying to separate upstream and downstream flanks. I created flanks with flankBed, and tried separating up and downstream flanks for forward and reverse strands using this code:

#Select forward strands
#Separate upstream and downstream flanks
!grep "+" Mcap.GFFannotation.flanks.gff \
| awk '{ if (NR%2) print > "Mcap.GFFannotation.flanks.forwardUpstream.gff"; \
else print > "Mcap.GFFannotation.flanks.forwardDownstream.gff" }'

I repeated this with reverse strands, then used cat to create an upstream track for all upstream flanks and a downstream track for all downstream flanks. Looking at IGV, I can tell this code does not work for all genes.

My guess is that some genes only have a single associated flank (up or downstream), so trying to separate every other flank entry as an upstream or downstream flank is causing these inconsistencies.

How can I correctly separate upstream and downstream flanks for forward and reverse strands?

Looking at flankBed documentation I tried using -l on its own, but that did not work.

[yaaminiv]

IGV file here, screenshots for reference:

good:

bad:

[shellywanamaker]

@yaaminiv I would not use your previous output to generate these. I would run flankbed again with the options

for upstream flanks:

-l 1000
-r 0
-s

and for downstream flanks:

-l 0
-r 1000
-s

[yaaminiv]

@shellytrigg Thanks!!! Wish they had more pictures for how -s works in the documentation