Extended Data Fig. 2: Updated transcriptome annotation improves the quality of processed scRNA-seq data.
From: An atlas of rabbit development as a model for single-cell comparative genomics
a, The distances of intergenic reads to their nearest annotated gene in a single GD8 sample. i) The distances for a subset of intergenic reads aligned to a region of chromosome 1 are shown. The vertical line indicates the 600 bp extension added to the 3′ ends (see Methods). ii) Distances are also shown for intergenic reads whose closest annotated gene is GATA1 and SOX9. b) The read coverage for the same GD8 sample shows that many reads associated with FOXA2 transcripts are positioned off the 3′ end of the OryCun 2.0 reference annotation. These missing reads are captured by our 600 bp extension. c) The 3′ extended gene annotations substantially improve the signal obtained after processing with Cell Ranger. d) Examples of new annotations added from aligning human gene annotations with the rabbit transcriptome. These new annotations overlap positions with high read coverage. e) The signal captured as a result of the new human gene annotations are consistent with the known expression patterns of SIX3 (forebrain marker) and FOXC1 (mesodermal marker). Intergenic read distances and normalised expression values are available in the source data.
