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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 6 months ago

nzhun commented 8 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 8 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 8 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 8 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 8 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: @.***