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TPM and Counts function not working as intended #84

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z5310969 opened this issue Feb 16, 2025 · 0 comments
Open

TPM and Counts function not working as intended #84

z5310969 opened this issue Feb 16, 2025 · 0 comments

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@z5310969
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Was testing out the tool in a docker container using the sample fastq files.

Used these commands to get TPM and count expression data for different expression measures

python SalmonTE.py quant --exprtype=count --reference=hs /data/CTRL_1_R1.fastq /data/CTRL_1_R2.fastq
and
python SalmonTE.py quant --exprtype=TPM --reference=hs /data/CTRL_1_R1.fastq /data/CTRL_1_R2.fastq

However, "count" data is showing significantly lower numbers compared to TPM when I believe it should be the other way around. Is this output expected or have I written down the command incorrectly?
Count
ALU,1.39182e-06
AluJb,1.92989e-05
AluJo,1.92989e-05
AluJr,3.90563e-07

TPM
ALU,0.0244029
AluJb,0.348222
AluJo,0.348222
AluJr,0.00675345

Any help is appreciated. Thanks in advance.

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