Table 1.

Bioinformatic pipeline speed evaluation. The table shows the speeds of our bioinformatic pipeline for four different runs on a bam file having ~200 million 76 nt-long stranded RNA-seq paired-end reads aligned to the human genome (GRCh37). The number of SINEs having an expression coverage over the calculated background signal (column 3) arises from different ‘-bg’ parameters in column 1 (see text for details). The step in the pipeline for expression coverage vector creation from the supplied bam file took almost 2 h.

-bg	SINEs Analysed	SINEs over Background	Identified Genuine Pol-III SINEs	Total Run Time (h)
3	430 k	2872	42	2.6
2	430 k	4576	119	2.8
3	1100 k	44,973	175	6.9
2	1100 k	64,425	463	10.9