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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
GNU General Public License v3.0
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coverage threshold for TE #21

Closed whiteorchid closed 3 years ago

whiteorchid commented 3 years ago

By the results, in the RepeatMaxCoverage column, some results items are 0. So does this means that LIONS will report all the TEs without a cutoff?

Thanks a lot!

ababaian commented 3 years ago

This is correct, all TE-exon interactions are reported the idea being that you as the researcher will set the cut-offs that you deem appropriate. As a general rule I go with at least 10-read support for a particular interaction.

It's an arbitrary heuristic, there are sensitivity-specificity trade-offs and 10 reads is is very close to the optimal (max AUC) distance when I did the benchmarking. There is no "correct" answer in this regard.