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Table 9 Comparisons of the number of predicted shared transcripts that are uniquely mapped (unique) or translocated (transloc) as reported by GMAP in the test on mouse against rat from Oases and from Mutual over different values of k and k-mer coverage cutoff c and over different e-value cutoffs 107 and 10−20 .

From: Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data

  mouse(10−7)   rat(10−7)
  Oases Mutual   Oases Mutual
k _ c unique transloc unique transloc k _ c unique transloc unique transloc
25_3 24635 599 (0.024) 30713 1475 (0.048) 25_3 21335 986 (0.046) 33566 2237 (0.067)
25_5 10718 436 (0.041) 12071 1011 (0.084) 25_5 8509 438 (0.051) 12676 971 (0.077)
25_10 2913 218 (0.075) 3197 409 (0.128) 25_10 2353 122 (0.052) 3042 257 (0.084)
31_3 20360 242 (0.012) 22229 483 (0.022) 31_3 18236 497 (0.027) 23818 795 (0.033)
31_5 8778 189 (0.022) 9263 388 (0.042) 31_5 7132 251 (0.035) 9453 388 (0.041)
31_10 1914 99 (0.052) 2026 176 (0.087) 31_10 1553 65 (0.042) 1888 113 (0.060)
  mouse(10 −20 )    rat(10 −20 )   
  Oases Mutual   Oases Mutual
k _ c unique transloc unique transloc k _ c unique transloc unique transloc
25_3 20209 544 (0.027) 24662 25 3 25_3 16880 746 (0.044) 25851 1536 (0.059)
25_5 9070 396 (0.044) 10067 25 5 25_5 7021 332 (0.047) 10097 718 (0.071)
25_10 2431 188 (0.077) 2631 25 10 25_10 1977 98 (0.050) 2499 214 (0.086)
31_3 16077 213 (0.013) 17610 31 3 31_3 13866 376 (0.027) 18290 516 (0.028)
31_5 7136 156 (0.022) 7538 31 5 31_5 5656 177 (0.031) 7572 243 (0.032)
31_10 1590 85 (0.053) 1701 31 10 31_10 1299 51 (0.039) 1559 83 (0.053)
  1. The number in parentheses is the ratio of the number of translocated transcripts to the number of uniquely mapped transcripts.