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nedialkova-lab / mim-tRNAseq

Modification-induced misincorporation tRNA sequencing
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Interpretation of the "proportion" Column in mismatchTable.csv #73

Closed Xinkai-Wu closed 2 months ago

Xinkai-Wu commented 2 months ago

Hello. I am a bit confused while interpreting the output file from mim-tRNASeq. The mismatchTable.csv lists the proportions of four types of bases at each position. However, why is the sum of the proportions for the four bases not equal to 1? Thanks!

Below is an example from the test data.

isodecoder canon_pos pos type proportion cov condition bam Homo_sapiens_mito_tRNA-Ala-TGC-1 1 1 A 0.0 534.0 HEK293T hg38_HEK239vsK562/mimseq_hek_1.unpaired_uniq.bam Homo_sapiens_mito_tRNA-Ala-TGC-1 1 1 C 0.0 534.0 HEK293T hg38_HEK239vsK562/mimseq_hek_1.unpaired_uniq.bam Homo_sapiens_mito_tRNA-Ala-TGC-1 1 1 G 0.0 534.0 HEK293T hg38_HEK239vsK562/mimseq_hek_1.unpaired_uniq.bam Homo_sapiens_mito_tRNA-Ala-TGC-1 1 1 T 0.0 534.0 HEK293T hg38_HEK239vsK562/mimseq_hek_1.unpaired_uniq.bam

Best, Xinkai

drewjbeh commented 2 months ago

Hi there. The mismatch table gives the proportion of misincorporation of each base at each position. The sum gives the total misincorporation at that position, not the total proportion of each base. There should be a NA value for each position and this refers to the reference nucleotide at this position. This is NA because you cannot count a misincorporation of the same base that was already there. For more info on output files please see https://mim-trnaseq.readthedocs.io/en/latest/output.html

On Tue, 17 Sept 2024, 23:12 Xinkai, @.***> wrote:

Hello. I am a bit confused while interpreting the output file from mim-tRNASeq. The mismatchTable.csv lists the proportions of four types of bases at each position. However, why is the sum of the proportions for the four bases not equal to 1? Thanks!

Below is an example from the test data.

isodecoder canon_pos pos type proportion cov condition bam Homo_sapiens_mito_tRNA-Ala-TGC-1 1 1 A 0.0 534.0 HEK293T hg38_HEK239vsK562/mimseq_hek_1.unpaired_uniq.bam Homo_sapiens_mito_tRNA-Ala-TGC-1 1 1 C 0.0 534.0 HEK293T hg38_HEK239vsK562/mimseq_hek_1.unpaired_uniq.bam Homo_sapiens_mito_tRNA-Ala-TGC-1 1 1 G 0.0 534.0 HEK293T hg38_HEK239vsK562/mimseq_hek_1.unpaired_uniq.bam Homo_sapiens_mito_tRNA-Ala-TGC-1 1 1 T 0.0 534.0 HEK293T hg38_HEK239vsK562/mimseq_hek_1.unpaired_uniq.bam

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Xinkai-Wu commented 2 months ago

Hi Drew, thank you for your response.