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Table 1 Comparison of total number of junctions identified by RSR for five cases from Tg and Dtt treated samples

From: Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

  Parameter Case 1 Case 2 Case 3 Case 4 Case 5
Variable Name Minimum split size 8 11 11 15 18
Maximum candidate distance 40,000 40,000 50,000 50,000 50,000
Read mapping region boundary buffer size 5 5 5 8 8
Minimum candidate distance 2 2 2 2 2
Minimum number of supporting reads 2 2 2 2 2
Maximum good alignment allowed per read 8 11 11 15 18
Tg Het Total number of junctions identified 122 140 143 135 141
Tg KO Total number of junctions identified 153 177 177 170 177
Dtt Het Total number of junctions identified 6496 6614 6661 6673 5683
Dtt KO Total number of junctions identified (Novel/Known) 6135 6247 6285 6308 5687
  1. The bolded numbers show parameters with different test settings