Bad examples of smudgeplot

[KamilSJaron]

A collection of smudgeplots that went wrong... (a material for a wiki page showing potential pitfalls)

Types of problems:

• a problem of input data
• a problem of input parameters
• a problem of smudge annotation

[KamilSJaron]

(problem with data) 2 species, one octoploid, one diploid were mixed together (I accidentally pulled a wrong library from ncbi)

[KamilSJaron]

[KamilSJaron]

There are so many bad examples here: #58 (comment)

[KamilSJaron]

[gemmacol]

Hi Kamil, it looks like I am producing "bad examples" as well.. I am not sure if this is an issue with the data or something I'm doing wrong with the plotting? These are illumina reads.

smudgeplot.py all kmerpairs_text.smu

GenomeScope version 2.0
input file = kmer.hist
output directory = .
p = 2
k = 21
NUM_ROUNDS = 1

property min max
Homozygous (aa) 97.3501% 97.5185%
Heterozygous (ab) 2.48152% 2.64989%
Genome Haploid Length 3,330,571,568 bp 3,415,771,847 bp
Genome Repeat Length 1,313,133,735 bp 1,346,725,374 bp
Genome Unique Length 2,017,437,834 bp 2,069,046,473 bp
Model Fit 78.2103% 95.5158%
Read Error Rate 0.559719% 0.559719%