Feature Request - Add 3' end match for RPFs

zhpn1024 / ribotish

Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data

http://dx.doi.org/10.1038/s41467-017-01981-8

GNU General Public License v3.0

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Feature Request - Add 3' end match for RPFs #10

Closed alanlorenzetti closed 2 years ago

alanlorenzetti commented 4 years ago

Hi. This is a great tool!

The prokaryotic community could benefit more of it if a feature doing the same for 3' end of RPFs could be added. Seems like the 3-nt periodicity for model organisms like E. coli is easier to notice when using 3' end profile of RPFs.

Thanks!

zhpn1024 commented 4 years ago

Do you mean taking 3' end of RPF as positions in quality figure?

alanlorenzetti commented 4 years ago

Yes. Please, check Figure 6 from this paper.

zhpn1024 commented 4 years ago

Got it. Do you want to assign P-site offset relative to 3' end?

alanlorenzetti commented 4 years ago

Oh, that is up to you. I don’t have sufficient expertise on the topic to judge whether this is a crucial feature. Sorry.

zhpn1024 commented 2 years ago

The feature has been added as option '--end3' in 0.2.6.

alanlorenzetti commented 2 years ago

Thank you!