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wshuai294 / PStrain

Pstrain profiles strains in metagenomics data. It infers strain abundance and genotype for each species. Also, it has a single species mode; where given a BAM and VCF, it can phase the variants for any species.
MIT License
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How to make a marker gene? #3

Closed zckoo007 closed 3 years ago

zckoo007 commented 3 years ago

Hi Shuai

I have a new genome, but I don't know how to make genome to marker gene. Can you give me some idea?

Bests Chengkai

wshuai294 commented 3 years ago

Hi Chengkai,

I think there are three possible solutions. First, you could map the new genome to the metaphlan database, and check if there is a hit. Maybe the new genome's marker gene is already in the database. Second, you could use PStrain's single species mode, you can use Bwa to map your reads to the genome, and call SNP by yourself. Then you can run PStrain with the bam and vcf file. You can find the single species mode tutorial in the readme file. However, the homologous regions from other species may affect the results. Finally, you can follow the metaphlan's method to build your own marker gene database. However, it would cost a lot of effort.

Please let me know if it helps.

Sincerely, WANG Shuai