Different outputs webtool vs python package?

[francoiskroll]

Sorry about the many questions!

Let's say I try exactly the same input with both the webtool & the Python package.

Webtool

Top predicted pegRNA is

• gN19 = GCTCGGCGAGCGACTACTGT
• sPBS_RTSeq = AGCGACTACTGTAGGTCGTCATGGGGCCGAA
• DeepPrime_score = 16.006807

Python package

pegrna = DeepPrime('test',
                   'TTTTGGGTTTTATCCTACAGCCCGTCATCGGCTCGGCGAGCGACTACTGTAGGTCGTCATAAGGCCGAAGGAGACCGTACATACTCTTACTGGGGATTCTGATGTTAGTGGGCATGACTTT',
                   'TTTTGGGTTTTATCCTACAGCCCGTCATCGGCTCGGCGAGCGACTACTGTAGGTCGTCATGGGGCCGAAGGAGACCGTACATACTCTTACTGGGGATTCTGATGTTAGTGGGCATGACTTT',
                   edit_type='sub',
                   edit_len=2)

pe2_output = pegrna.predict(pe_system='PE2', cell_type='HEK293T')

Top predicted pegRNA is

• gN19 = GCTCGGCGAGCGACTACTGT
• sPBS_RTSeq = TTCGGCCCCATGACGACCTACAGTAGTCGCT (which is exactly reverse-complement of webtool output)
• PE2_score = 15.269821167

I guess the top-predicted pegRNA is the same in both cases, but the score is slightly different? Anything I should worry about?

[Goosang-Yu]

The response of issue #45 might be helpful.

In short, if you have to choose one, I recommend using GenET. GenET is actively maintained, with discovered bugs being fixed, and it receives regular updates.

[francoiskroll]

Yes that perfectly answers my question. Sorry I hadn't seen it!