Extended Data Fig. 5. Gene expression and read assignment with extended references.

(a) Scatter plots comparing gene expression of Illumina and Ultima datasets using extended references for both. Extended references from bulk RNA-seq (bulk) or Ultima scRNA-seq (SC). Labeling as in Fig. 2e. For 5′ data we used the reference extended by 5′ Ultima data, while for 3′ data we used the reference extended by 3′ Ultima data. (b) Same as (a), except using the standard reference for Illumina in all cases. (c) Same as (a), except comparing standard with extended references for the same dataset. (d) Bar plots showing classification of reads by FeatureCount, both with the standard reference and with the extended references. Categories as in Extended Data Fig. 4. Reads were sampled so that Illumina and Ultima have the same number of reads.