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MrOlm / inStrain

Bioinformatics program inStrain
MIT License
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clarity regarding strain_clusters.tsv #166

Closed ShailNair closed 11 months ago

ShailNair commented 11 months ago

Hi,

Thanks for the all the hard work that has been put into developing instrain package. It has substantially aided my research into exploring the genetic diversity within the population i am currently studying. I conducted a comparison of the Instrain profiles of metagenomic assembled virus contigs/genomes across days, which were dereplicated at 95% ANI. I got the following strain_clusters.tsv table:

<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

cluster | sample | genome -- | -- | -- 1_1 | 100.days.sort.bam | c_000000000018.fasta 1_1 | 250.days.sort.bam | c_000000000018.fasta 1_1 | 400.days.sort.bam | c_000000000018.fasta 1_1 | 450.days.sort.bam | c_000000000018.fasta 1_2 | Original.bottle.sort.bam | c_000000000018.fasta 2_1 | 400.days.sort.bam | c_000000000022.fasta 2_1 | 450.days.sort.bam | c_000000000022.fasta 6_1 | 100.days.sort.bam | c_000000000058.fasta 6_2 | 250.days.sort.bam | c_000000000058.fasta 6_3 | 400.days.sort.bam | c_000000000058.fasta 6_3 | 450.days.sort.bam | c_000000000058.fasta 6_4 | Original.bottle.sort.bam | c_000000000058.fasta

Based on the provided description, I infer that the number preceding the underscore in "cluster" column represents cluster number/serial number. While the number after the underscore represents strain number. For example, in the case of "c_000000000018.fasta," the strain appears to be similar in the first four samples but different in the last one. Likewise, concerning "c_000000000058.fasta," the strains differed across all samples except for '400.days.sort.bam' and '450.days.sort.bam.'

Is this interpretation correct?

MrOlm commented 11 months ago

Hi @ShailNair - yes, your interpretation is correct.

Best, Matt

ShailNair commented 11 months ago

Thanks Matt