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diriano / ploidyNGS

Explore ploidy levels from NGS data alone
GNU General Public License v3.0
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#Not an issue, but needed help to comment on ploidy of an organism. #7

Closed bhagya-ct closed 6 years ago

bhagya-ct commented 6 years ago

Dear Developer,

sorry to raise an issue unnecessarily.

Below is what I got when I ran the tool, (.venv) mml@MML:~/softwares/ploidyNGS$ ./ploidyNGS.py --guess_ploidy -o guess_test -b dedup_SS_BWA_reads.bam ###############################################################

This is ploidyNGS version v3.1.2

Current date and time: Tue Nov 14 22:13:57 2017

############################################################### BAM index present... OK! Number of mapped reads from BAM: 3483177 Observed average coverage: 54.00 Coverage used for guessing ploidy: 50

After comparing your data with our simulated dataset and computing the Kolmogorov-Smirnov distance, the closest ploidy to yours is 3

And the image generated is attached below.

In the scientific field, confusion is haploid? or diploid?

Little information about the organism: Fungi, 12.5mb genome, Illumina Miseq paired end reads.

Please go through the image and let me know what do you think.

Thanks Bhagya C T

guessnoidea_test_depth100.tab.PloidyNGS.pdf

diriano commented 6 years ago

Dear Bhagya,

no need to raise an issue for this. You can contact us via e-mail. Check our paper to get the contact details.

Did you mask your genome? That is important to eliminate false polymorphisms. Perhaps trying individually on the largest contigs will give a clearer idea.

Cheers, Diego