Closed tanpham15 closed 3 months ago
I'm not entirely sure what kind of output you are expecting for the plot. Is it that you expected to see more connections?
In this case, I would not increase maxGap
too much. It basically merges together links but it also gives fairly strange results (e.g. CHR31 to the bottom contig, merging together very distant small links). Keeping minBundleSize=1
is probably be fine.
I filter based on the MAPQ. Maybe lowering the MAPQ
threshold could help to recover mapped sequences thus retaining more links.
Also, for your purposes, it may actually be beneficial to actually run the pipeline with the reference and contigs in reverse. If not to see what it looks like.
Stale
Dear Justin Chu and authors,
When I changed the parameters of minimap2 (from asm10 -> asm20) it helped to increase the connection, and it looks similar to result from nucmer dot plot.
However, there is only a weird connection, but it make the figure become nonsense. Please take a look these figures bellow are results from minimap2 with asm10 and asm20
Could you please let me know how can I fix it? P/S: I used
minBundleSize=1
andmaxGap=9999999999
from the previous issues https://github.com/JustinChu/JupiterPlot/issues/38