FPKM counts are more than Tot_counts in Squire Count output.

[Surar]

Dear all,

I hope you are fine, I have used SQuIRE to quantify TEs. the data are fine for most of the samples except for the RNA seq taken from two cell lines (C8161 and fibroblast (3 samples for each cell line)). squire Count results showed much more counts in the FPKM column than the corresponding Tot_counts. any idea what might cause this? I didn't get any error message after running the script but the results are confusing.

Many thanks and best regards
Surar