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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
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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