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Table 4 Comparisons of results from using single-end and paired-end reads for finding fusions

From: TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

Read type Fusion genes (left-right) Chromosomes (left-right) 5' position 3' position Spanning reads (RPM) Spanning pairs
Single GAS6-RASA3 13-13 114529968 114751268 15 (0.267)  
Paired GAS6-RASA3 13-13 114529968 114751268 10 (0.198) 43
Single BCR-ABL1 22-9 23632599 133655755 6 (0.107)  
Single BCR-ABL1 22-9 23632599 133729450 3 (0.053)  
Paired BCR-ABL1 22-9 23632599 133655755 2 (0.040) 7
Paired BCR-ABL1 22-9 23632599 133729450 3 (0.059) 10
Single ARFGEF2-SULF2 20-20 47538548 46365683 17 (0.302)  
Paired ARFGEF2-SULF2 20-20 47538545 46365686 10 (0.198) 30
Single BCAS4-BCAS3 20-17 49411707 59445685 25 (0.445)  
Paired BCAS4-BCAS3 20-17 49411707 59445685 13 (0.257) 145
  1. Comparisons of single-end and paired-end reads as evidence for gene fusions in the Universal Human Reference (UHR) cell line (a mixture of multiple cancer cell lines), using the known fusions GAS6-RASA3, BCR-ABL1, ARFGEF2-SULF2, and BCAS4-BCAS3. With TopHat-Fusion's ability to align a read across a fusion, the single-end approach is competitive with the paired-end-based approach. RPM is the number of reads that span a fusion per millon reads sequenced. For instance, the RPM of single-end reads in GAS6-RASA3 is 0.267, which is slightly better than the RPM for paired-end reads. Single-end reads may show higher RPM values than paired-ends in part because single-end reads are longer (100 bp) than paired-end reads (50 bp) in these data, and therefore they are more likely to span fusions.