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wurmlab / flo

Same species annotation lift over pipeline.
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Results and discussion #20

Closed mictadlo closed 3 years ago

mictadlo commented 6 years ago

Hi, How did you calculate the below percentage?

For an ant genome (~350 Mb) we saw 90% annotations map identically to the new assembly (unpublished result).

Is it possible to get more statistics out of Flo?

Thank you in advance.

Michal

yannickwurm commented 6 years ago

Wait who are you working with?

mictadlo commented 6 years ago

I am working with plants and I was just wondering how I could calculate similar statistics from flo results.

mictadlo commented 6 years ago

Did I choose the right data to calculate how much annotations map identically to the new assembly?

ls
input.cds.fa  input.gff  lifted_cleaned.cds.fa  lifted_cleaned.gff  lifted.gff3  unlifted.gff3  unmapped.txt

> grep "ID=" unlifted.gff3 | wc -l
19233
> grep "ID=" lifted_cleaned.gff | wc -l
33639
> wc -l unmapped.txt 
43632 unmapped.txt
> grep "ID=" input.gff | wc -l
45857
> python 
>>> float(33639*100)/45857
73.35630329066446

Thank you in advance,

Michal