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

BMC Bioinformatics

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

Assembly	№ of *bona fide* UTF	№ of chimeras in unmapped transfrags ζ	Alignment of TF to reference genes (CDS)				Alignment of TF to reference genome
Assembly	№ of *bona fide* UTF	№ of chimeras in unmapped transfrags ζ	№ 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

^†Bona fide: transfrags with coding potential and predicted CDS.
*Orphan: transfrags with no coding potential or with coding potential but no predicted CDS.
ζ Possible chimera with a distinct breakpoint.

ISSN: 1471-2105