VDJ Region Coverage and assembleContigs

[bshim181]

I have been seeing some discrepancies between the percentage of reads that have full VDJ region coverage and the percentage of clones that demonstrate succesfully assembly of VDJ region contigs.
This is a nanopore data and I utilize generic-ont preset with
--assemble-contigs-by VDJRegion parameter.

This is the number I see within assembleContigs Report.

I expected higher percentage of clones to have successfully assembly of contigs since high percentage of reads demonstrate alignment till the VDJ region. Why might this be the case?

[mizraelson]

Answered in #2017