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padlocbio / padloc-db

HMMs and system models used by PADLOC
MIT License
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Target coverage threshold #6

Closed rfarouni closed 2 years ago

rfarouni commented 2 years ago

Hi,

It seems to me that the HMMs for the RT genes icity0039, icity0040 have a target coverage threshold in the meta file that is too high. I would set it to 0.3 so it would be easier to detect an RT in a fusion gene. I was experimenting with your thresholds and I discovered that I missed a well-known cas-rt fusion gene with the set threshold of 0.5.

Rick,

JacksonLab commented 2 years ago

Hi Rick,

Thanks for raising this, appreciate feedback from users. I've made a note to update these cutoffs with the next db release (so the change carries over to the precomputed dataset on the webserver as well).

Cheers,

Simon