Question on prepare-orfs "--longest" flag

smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data

http://doi.org/djv4

GNU General Public License v3.0

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Question on prepare-orfs "--longest" flag #137

Closed ericmalekos closed 1 year ago

ericmalekos commented 1 year ago

I understand the stated behavior of the "--longest" flag to choose the 5' most, in-frame start codon. What if this flag is not set? Are all ORFs returned?

saketkc commented 1 year ago

That's correct, all possible ORFs are retained in the index.