Fig. 5

Comparing RNA-seq and transcript counting. The genes identified as showing differential transcript abundance in experiment lamc1 ^sa379 with an adjusted p-value <= 0.05 and an absolute fold change of >= 2 by one or both methods at the less stringent proximity filter between the transcript counting 3′ end (TC 3′ end) and the Ensembl transcript end (Table 1 row 16) were plotted with their log₂ fold change from RNA-seq against the log₂ fold change from TC. Genes with an adjusted p-value <= 0.05 and absolute fold change >= 2 in both RNA-seq and TC are shown as blue circles. Genes which fail on one or both criteria in RNA-seq but not in TC are shown as green circles and vice versa as red circles. a The log₂ fold changes of genes with the TC 3′ end and Ensembl transcript proximity filter between -100 and +5000. The arrows highlight examples of genes which are not seen in graph B. b The log₂ fold changes of genes with the proximity filter between -100 and +100. c A table showing the number of genes represented by each circle colour. The fourth and fifth columns show the genes which are lost during the more stringent proximity filtering and whether these are considered true positives or false positives after examining the TC 3′ end. Note that for two genes where the RNA-seq and TC data correlated, the closest TC 3′ end was found to be false, but a true end was identified further downstream and indicated by square brackets. The number in curly brackets indicates genes with a true TC 3′ end and an absolute fold change >2 but which fail to show an adjusted p-value <= 0.05 in TC