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Table 1 Results of Solexa/Illumina paired-end reads (75nt in length) assembled by Trinity

From: Dissecting organ-specific transcriptomes through RNA-sequencing

Sample Number of raw reads Number of contig entries N50 Reads assembled % Reads usage Annotated (full+partial)*
(1e-5)
A 19874108 50284 1454 17483903 88% 15707+22815
B 20599558 55164 1288 17812061 87% 14954+27058
C 19710038 52538 1221 17177667 87% 12816+26672
D 20406514 46799 1214 17847745 88% 11134+24364
E 23228336 48568 1336 20655630 89% 14143+22263
F 38954816 63811 1426 32331937 83% 18431+27754
Total   90451 1209    23474+39539
  1. Each sample was handled with the default parameters in Trinity from cleaned raw data. The sample "Total" was obtained by combining all contigs of the six samples above and assembling them further via TGICL. The number for reads integrated into assemblies was calculated from the number of reads that are alignable to contigs at levels of more than 93% (>=70/75).
  2. *Annotated in full are the contigs showing both ATG and STOP codons, while partial refers to the rest of the contigs. All comparisons were performed against the reference sequences at the e-value indicated.