Add imputed sequences for exportAIRR

[racng]

Is there a way to export imputed sequences in AIRR format?
Imputation for full transcript sequences is extremely helpful for things like cloning. At the same time, AIRR format is a file format that can be parsed easily by analyses software, like scirpy. It would be great if we can have both of these features in one output!

Thank you!

[racng]

Actually, I realized that I could run extend before exportAIRR and that should mostly solve the problem. The only drawback is that the imputed values are also in uppercase.

mixcr extend --v-anchor L1Begin --j-anchor FR4End sample.clns sample.extended.clns
mixcr exportAirr sample.extended.clns sample.airr.extended.tsv

How do I add extend step to a preset file? Would the algorithm know to exportAirr/exportClones from the extended .clns file?

[mizraelson]

Hi, do you mean to add extra column to AIRR output, similar to the imputed sequence column you get with exportClones? We can do that.

[racng]

Instead of extra columns, can it be stored in the corresponding field without the "nImputed" prefix? For example, have the imputed sequences stored under columns: cdr1, cdr2, cdr3, fwr1, etc.? Also does the imputation also fill out the position values for start and end of these sequences as well?

[mizraelson]

That is possible, we will add this feature to the develop version in a few days.
You mean if start and end will represent the imputed sequence?

[racng]

Yes. Can we have the option to have the "_start" and "_end" fields represent the imputed sequences?