TRA TRD clones

[christoforos-dimitropoulos]

Hello,

I have used the analyze shotgun in order to align some bulk RNAseq data and I further used the "exportClones -c TRA" function in order to export the TRA clones. As you know this results in a combination of alpha and delta clones. Is there any good way of distinguishing those two?
Thanks a lot

[dbolotin]

Hi, please see this answer. Basically this task is fundamentally tricky, especially tricky for data like RNA-Seq where you have C genes only for some sequences. Still we will soon add some more flexibility in that sense that there will be easier to export those clones which certainly are TRA, because they were aligned with TRAC gene. Now you can do the same by manually filtering only those clonotypes which have TRAC / TRDC gene.

[christoforos-dimitropoulos]

Hey again, thanks for the info!
Is there an easy way of filtering out these TRD clones? I used the -c TRA parameter in exportClones but didnt seem to actually filter those out.