Fig. 2

Sequencing depth is positively correlated with transcript count and sensitivity in human pluripotent stem cells. A-C. Number of reads versus the number of transcripts assembled from 150 computationally verified hPSC samples. The numbers of all hPSC transcripts (A), coding transcripts (B) and noncoding transcripts (C) are shown on the vertical axes. The lines indicate the loess fits with standard error bands shown. Rho is the Spearman rank correlation coefficient. The distributions of the samples are shown on the axes. D. Number of reads versus the coding to noncoding ratio. E. Increment in the number of transcripts per additional 10 million reads. The numbers of transcripts are predicted from the loess fits in panels A-C. F. Sensitivity versus the number of reads using unfiltered transcript set assembled from the merged alignment of all the 150 hPSCs. G. Sensitivity versus the number of reads using only GENCODE-annotated assembled transcript set. The hPSC transcripts that were not found in GENCODE annotation were excluded. H. Sensitivity versus the number of reads using hPSC assembly. The hPSC assembly, published in Babarinde et al. includes additional transcripts that were not found in GENCODE annotation but excludes GENCODE transcripts that are not expressed in hPSCs. I. The number of samples in which the transcripts are assembled. For each category of transcripts, the number of samples for which the transcripts were correctly assembled was computed