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mourisl / T1K

T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.
MIT License
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readout of the output #25

Closed nzhun closed 9 months ago

nzhun commented 11 months ago

Hi, can you tell me how to read the output file, especially for the *_genotype.tsv? how to filter this file for true positive calls?

thank you,

mourisl commented 11 months ago

The simplest usage is to in the genotype.tsv file as a dataframe, and get the 3rd and 6th columns if the corresponding 5th and 8th column values are greater than 0.

nzhun commented 11 months ago

Thank you for the reply, could you explain what the columns are?

On Dec 14, 2023, at 5:01 PM, Li Song @.**@.>> wrote:

The simplest usage is to in the genotype.tsv file as a dataframe, and get the 3rd and 6th columns if the corresponding 5th and 8th column values are greater than 0.

— Reply to this email directly, view it on GitHubhttps://github.com/mourisl/T1K/issues/25#issuecomment-1856744015, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AENMOQZRMV5JOWMPXSM3BA3YJNZMXAVCNFSM6AAAAABAVQQNG2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJWG42DIMBRGU. You are receiving this because you authored the thread.Message ID: @.***>

mourisl commented 11 months ago

These columns are for "gene_name num_diff_alleles allele_1 abundance_1 quality_1 allele_2 abundance_2 quality_2 secondary_alleles". You can find more details in the README at https://github.com/mourisl/T1K?tab=readme-ov-file#inputoutput

nzhun commented 11 months ago

Very helpful, thank you

On Dec 14, 2023, at 5:53 PM, Li Song @.***> wrote:

These columns are for "gene_name num_diff_alleles allele_1 abundance_1 quality_1 allele_2 abundance_2 quality_2 secondary_alleles". You can find more details in the README at https://github.com/mourisl/T1K?tab=readme-ov-file#inputoutput

— Reply to this email directly, view it on GitHubhttps://github.com/mourisl/T1K/issues/25#issuecomment-1856870060, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AENMOQ4W3UN4F64WHIU342DYJN7OXAVCNFSM6AAAAABAVQQNG2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJWHA3TAMBWGA. You are receiving this because you authored the thread.Message ID: @.***>

Na Zhu, PhD Associate Research Scientist, Chung Lab, Department of Pediatrics Shen Lab, Department of Systems Biology Columbia University email: @.***