Table 2.
Characterization of transcriptome assembly via Trinity.
| Trinity Assignments | Number of contigs with hits or assignments |
|---|---|
| Total Illumina raw reads | 1,066,291,200 |
| Total number Trinity assembled contigs | 224,631 |
| Number of clusters (95%-CD-HIT-EST output) | 205,243 |
| Filtering using EdgeR to eliminate low expression contigs (reference transcriptome) | 69,002 (33.61%) |
| Total trinity ‘genes’ | 56,110 |
| Total trinity transcripts (-ERCC spike-ins) | 68,929 |
| Median contig length in bp | 940 |
| Contig (N50 in bp) | 1,997 |
| Average contig in bp | 1,364 |
| Number of predicted peptides (Transdecoder) | 66,167 |
| Transcripts after RUVg filtering (filtered_transcriptome) | 35,696 (51.73%) |
| Differentially expressed (DE) | 8,706 (24.38%) |