Comments (3)
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.
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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
from smudgeplot.
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.
from smudgeplot.
Related Issues (20)
- unclear if genome is a diploid (Smudgeplot) or pentaploid (PloidyPlot)? HOT 4
- Problems compiling (and running) smudge_pairs HOT 5
- Process was automatically killed HOT 3
- none results generating with huge dump files HOT 6
- smudgeplot.py hetkmers massive memory and walltime required HOT 3
- Interpretation of (maybe) hybrid genomes - multiple species HOT 1
- ploidyplot never finishes HOT 2
- script execution never ends HOT 2
- Error in estimate_1n_coverage_1d_subsets(total_pair_cov, minor_variant_rel_cov) HOT 2
- solve speckiness problem of smudgeplot HOT 2
- unable to start device PNG HOT 1
- plot err HOT 3
- Interpreting a possible haploid HOT 5
- Hexaploid Plant Analysis and Genome Assembly Questions HOT 2
- SPloidyPlot detecting two smudges at the same positions warning HOT 4
- Error while plotting Smudgeplot HOT 3
- script execution never ends (Extremely Large .jf Files) HOT 1
- Hexaploid plant interpretation and coverage HOT 2
- quantile filtering does not take freq into account
- PloidyPlot: Table part ./.finall.ktab.1 is missing ? HOT 1
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