Dereplication of RESCRIPt


When I perform

qiime rescript dereplicate ...

When tool found identical seqs -- will command filter out random ones from them? Or it would keep sequences with more frequent taxonomy labels ( which I would expect) ?

Thanks for your attention :slightly_smiling_face:

If you run the command qiime rescript dereplicate --help, you will see descriptions for several options. By default the uniq option is used. That is, if several sequences are identical, yet each has a uniq taxonomy, then each sequence is retained.

More details can be found here, click on the drop-menu for "Dereplication considerations" for additional information.

1 Like

@SoilRotifer thanks

just wondering there is for example option "super" - will it use only taxonomy information or sequence information too?

If no (or just in general) - are you going to some options based on sequences analysis? For example it looks like good idea --- if we have two species with same sequence -- we could analyze another sequences of these species and find out sequences of which species are closer to that one. So on that analysis it would be possible to rip out some undesirable records. Of course it is not only possibility to use sequence analysis. Another possibility for example just rip out some rare strnge records ( I mean with rare strange taxonomy )

Much of this is addressed in the RESCRIPt tutorials and the paper. You may consider reading about q2-clawback too.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.