Scisorseqr and MAS-Seq reads

[goeringr]

Has anyone used scisorseqr with segmented MAS-seq reads from PacBio?

I didnt think this would affect the read structure much but I am detecting very low Barcode content:

Total reads >= 200 bp: 698475 poly_T_found: 665397 Percent poly_T_found: 95.2643 poly_T_not_found: 33078 Percent poly_T_not_found: 4.73575 Unique Barcodes : 50 Reads with barcode: 162 Reads with barcode given polyA: 0.024364 Percent barcoded reads: 0.231934 Percent TSO found: 96.8675 Percent doubleTSO: 0.00801747 Average barcoded read length: 641.667 Average read length of file: 670.152

I'm using a 1M subset of the segmented reads and 1887 Barcode-celltype assignments