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

[noush-joglekar]

This is very late - sorry! I have not used scisorseqr with MAS-seq, but these seem like very low numbers. Have the reads been de-duplicated / deconvolved or are these raw fastqs from the PacBio machine?

[goeringr]

Oh it has been a while... The reads were downstream of segmentation (skera) but upstream of all trimming/deconvolution (lima)