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alexcritschristoph / soil_popgen

Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes
GNU General Public License v3.0
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Generate inStrain object for fst calculation #9

Closed ChenTianYi99 closed 5 months ago

ChenTianYi99 commented 5 months ago

Hi, i have run inStrain to profile microdiversity of viral populations and the tool produced a variety of output in the "NAME_profile" folder (scaffold_info.tsv, gene_info.tsv, genome_info.tsv, linkage.tsv, mapping_info.tsv, scaffold_info.tsv, SNVs.tsv).

In downstream analyses, i tried to use fst.py to calculate Fst values for paired species but i could not find "Name_profile.data". Should i run inStrain_lite to generate this file instead of inStrain?

Thanks in advance.

alexcritschristoph commented 5 months ago

Probably the best route here would be to write some new python code with scikit-allel to calculate Fst from the inStrain SNVs table.