search

JustinChu / JupiterPlot

A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.
GNU General Public License v3.0
68 stars 11 forks source link

Effect of mapping parameters #43

Closed tanpham15 closed 3 months ago

tanpham15 commented 8 months ago

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. nucmer_dotplot

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 plot_ver4_asm10 jupiterplot_asm20

Could you please let me know how can I fix it? P/S: I used minBundleSize=1 and maxGap=9999999999 from the previous issues https://github.com/JustinChu/JupiterPlot/issues/38

JustinChu commented 6 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.

JustinChu commented 3 months ago

Stale