failed to obtain the final plot

[Gon1976]

Hi
I install smudgeplot using conda. And also running the exec files directly.
I can obtain kmer-pairs_L_U_coverages.tsv, kmc_tools and smudgeplot.py hetkmers
But, finally I can run the last step to construct the graph (I think a library is missing in my R installation)

Error in library("argparse") : there is no package called ‘argparse’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Ejecución interrumpida

If I install the library in a personal library it will work? Or I need to ask the root to install the package?
thanks

[KamilSJaron]

Hi, I am a bit puzzled. I thought conda actually installs the package as well.

In any way, you should be able to install the package yourself and that should fix the problem.

[Gon1976]

Thanks! I can make the plots!

I a bit confused about how to select low and upper coverage filter. I try with different values according to warning message of smudgeplot:
!! Careful, your coverage filter on the lower end (L = 100 ) is higher than half of the 1n coverage estimate ( 1n / 2 = 54.55. Using this L filter the plot suggest diplod genome, I try using L 20 (pentaplid) and L10 (multiploidy).

How can extract L and U values from genomescope output?
thanks

[KamilSJaron]

Hi, check this wiki page in the documentation: https://github.com/KamilSJaron/smudgeplot/wiki/chosing-L-and-U

If it was unclear, i will try to clarify it.