Comparing SalmonTE output with TEtranscripts

[z5310969]

I am a student doing a project that involves comparing your tool SalmonTE against other TE quantification tools such as TEtranscripts.

So far, I have implemented SalmonTE and use this script to call it

python /opt/SalmonTE/SalmonTE.py quant --reference=hs --exprtype=count

Where there are 2 input files. A file labeled R1 for a sequence of RNA and an R2 file is the reverse.

I am currently comparing the outputs of both TEtranscripts and SalmonTE (using the above script) on the same input files. However, I am getting drastically different results.

Attached to the Issue are:

• The transposable elements (TEs) that are quantified in both tools and the counts that each tool gives for them.
  output_comparison_P012606_newWF.csv

• A scatter plot of the results in the spreadsheet
  

I was wondering if the script I used above is similar to what settings were used when TETranscripts and SalmonTE were compared to each other in the original paper.

Thank you in advance for your time and support.