Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA

Table 1 Comparative assessment of P. falciparum transcriptome assembly highlights the performance of Cufflinks RABT

	Contiguity	Chimerism	Total number of transcripts	Number of intergenic transcripts	Number of antisense transcripts
PlasmoDBv10.0			5,777
Cufflinks	81.5 %	6.6 %	7,065	660	479
Cufflinks RABT	100 %	4.5 %	9,434	660	474
Genome-guided Trinity	57.1 %	1.3 %	43,816	8,260	11,070
Genome-guided Trinity RABT	100 %	1 %	21,182	5,839	7,234

We compared the contiguity, chimerism, and feature counts of Cufflinks versus Genome-guided Trinity transcriptome assembly, with or without the assistance of annotation. Cufflinks incorporating reference annotation based transcriptome assembly (RABT) provided the optimal P. falciparum transcriptome.
Contiguity is the rate of annotated transcripts covered by one assembled transcript over at least 90 % of the annotated transcript exonic length in the correct orientation. Chimerism is the rate of assembled transcripts that span more than one annotated transcript in the correct orientation. Total number of transcripts, number of intergenic transcripts, and number of antisense transcripts correspond to the total number of assembled transcripts, the number of assembled transcripts predicted between PlasmoDBv10.0 annotations, and the number of assembled transcripts predicted antisense to PlasmoDBv10.0 annotations. In total, 5,777 transcripts are annotated in PlasmoDBv10.0
*RABT = Reference annotation based transcript assembly

ISSN: 1471-2164