I have encountered an issue with StringTie's quantification results that vary based on the use of the -e option. Specifically, I have observed a difference in the abundance file outputs for a gene when running StringTie with and without the -e option.
When I run StringTie with the -e option, the output in the abundance file shows zero coverage, FPKM, and TPM values for a gene (thrL) that has existing annotations:
Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM
gene-b0001 thrL NC_000913.3 + 190 255 0.000000 0.000000 0.000000
However, when I run the same command without the -e option, the output shows non-zero values for the same gene:
Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM
gene-b0001 thrL NC_000913.3 + 190 255 452.000000 158.843719 97.874275
Despite this, the corresponding GTF file still shows zero values:
Could you please help me understand why there is a variation in the quantification results for a gene with existing annotations, depending on whether the -e option is used or not? Additionally, why does the GTF file still show zero values despite the non-zero values in the abundance file when -e is not used?
Hello,
I have encountered an issue with StringTie's quantification results that vary based on the use of the
-e
option. Specifically, I have observed a difference in the abundance file outputs for a gene when running StringTie with and without the-e
option.When I run StringTie with the
-e
option, the output in the abundance file shows zero coverage, FPKM, and TPM values for a gene (thrL
) that has existing annotations:However, when I run the same command without the
-e
option, the output shows non-zero values for the same gene:Despite this, the corresponding GTF file still shows zero values:
Could you please help me understand why there is a variation in the quantification results for a gene with existing annotations, depending on whether the
-e
option is used or not? Additionally, why does the GTF file still show zero values despite the non-zero values in the abundance file when-e
is not used?Thank you for your assistance.