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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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Blank sections in preqc results #140

Closed genes-and-genomes closed 6 years ago

genes-and-genomes commented 6 years ago

Some datasets produce blank graphs for: variant branches in k-de Bruijn graph repeat branches in k-de Bruijn graph error branches in k-de Bruijn graph

Looking into the preqc files for these datasets that produce blank graphs, 'BranchClassification' is blank. See below for a normal preqc file and one with blank 'BranchClassification'. image image

I have not been able to identify a pattern for why some datasets produce all the graphs while some don't. I am running SGA 0.10.15.

jts commented 6 years ago

Hi,

If the sequencing depth is too low then the branch classifications may be inaccurate. When this situation is detected there will be no branch classifications output.

Jared