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drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
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Counter and control selection parameters #123

Open Jimaz opened 1 year ago

Jimaz commented 1 year ago

Hi! To carry out the analyses we are working on with APTASUITE, we would need some more information about the following options that can be used in the configuration file: SelectionCycle.isControlSelection and SelectionCycle.isCounterSelection. Could you please tell us what the difference is between these two parameters, that is, between considering the samples as control or counter selection? Cheers! Jaime

drivenbyentropy commented 1 year ago

A counter selection refers to any cycle in which the aptamers were incubated with molecules that are not the target and where those sequences that did not bind where kept for the next round. This for instance is useful in cell-SELEX in order to increase the specificity of potential binders.

A control selection refers to any selection that informs your SELEX protocol, eg incubation with a homolog. The resulting data (e.g. comparing enrichment of aptamers between control and selection cycle) can be useful to identify species that bind to both, or just one of the molecules.

I hope this helps!