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Table 4 Summary of bona fide † and orphan* transfrags integrity and validity

From: Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms

Assembly № of bona fide UTF № of chimeras in unmapped transfrags ζ Alignment of TF to reference genes (CDS) Alignment of TF to reference genome
№ of TF Cov 50%, ID 50% № of reference unigenes № of TF Cov 90%, ID 90% № of reference unigenes № of TF uniquely mapped № of N. crassa genes identified by TF
Trinity 14806 282 9879 6263 2593 1609 13339 7915
Oases-25 13834 469 8653 5699 1086 784 11679 7345
Oases-M 37681 3293 22080 5991 2751 1009 27931 7787
Oases-P 50445 3417 30278 6179 4115 1249 39693 7906
Trinity* 20772 49 5016 1887 4063 1543 18553 3875
Oases-25* 5359 22 1292 844 1008 679 4918 1287
Oases-M* 7453 268 1512 916 976 653 6148 1483
Oases-P* 10848 247 2355 1234 1458 882 9203 1919
  1. Bona fide: transfrags with coding potential and predicted CDS.
  2. *Orphan: transfrags with no coding potential or with coding potential but no predicted CDS.
  3. ζ Possible chimera with a distinct breakpoint.