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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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Consequences of diploid model #81

Closed karinlag closed 9 years ago

karinlag commented 9 years ago

Hi!

I really like the way PreQC presents the data, but I do have one question: you state in the paper that you use a diploid model.What consequences does that really have for the analyses? Does this mean that this tool should not be used for haploid organisms, for instance?

Thanks!

karin

jts commented 9 years ago

Hi Karin,

You can use it to analyse haploid genomes and I used a haploid yeast genome as an example in the paper. You just need to be aware of ploidy when you interpret some plots. For example the 'variation branch rates' plot for a haploid genome probably indicates systematic sequencing errors and/or paralogous sequence.

Jared

On Mon, Sep 22, 2014 at 3:31 PM, karinlag notifications@github.com wrote:

Hi!

I really like the way PreQC presents the data, but I do have one question: you state in the paper that you use a diploid model.What consequences does that really have for the analyses? Does this mean that this tool should not be used for haploid organisms, for instance?

Thanks!

karin

— Reply to this email directly or view it on GitHub https://github.com/jts/sga/issues/81.

jts commented 9 years ago

Hi Karin,

I'm going to close this issue. Please re-open if you have any followup problems.

Jared