Table 7 Comparison of assembly statistics from de novo (Velvet-Oases and Trinity) and reference (TopHat-Cufflinks) assemblers
Velvet-OasesTrinityTopHat-Cufflinks
Total no. of reads182,386,000182,386,000157,164,008
No. of initial transcripts601,915158,86375,237
No. of transcripts after removing isoforms43,81639,08453,632
Average size of transcript155411121310
Maximum transcript length26,06022,88716,681
Minimum transcript length10020194
N50221818631677
No. of transcripts in N50134,41128,90118,762
% of transcripts annotated678487
No. of novel transcripts detected14,54054646700