|  | v1 (k-mer = 25) | v2 (k-mer = 29) | v3 (k-mer = 32) | v4 |
---|
Total ‘gene’ count | 269,388 | 238,782 | 226,402 | 42,040 |
---|
Total transcript count | 512,945 | 471,767 | 451,199 | 113,893 |
---|
All Transcripts | Contig N50 | 762 | 926 | 1029 | 1709 |
Median Contig Length | 390 | 424 | 448 | 1094 |
Average Contig Length | 598.54 | 669.21 | 713.94 | 1317.45 |
Longest Isoform | Contig N50 | 662 | 747 | 792 | 1816 |
Median Contig Length | 359 | 371 | 375 | 998 |
Average Contig Length | 549.32 | 590.09 | 609.47 | 1301.70 |
- Trinity (version 2.0.6, [24]) was used to generate three unique de novo waterhemp transcriptome assemblies: v1, v2, and v3 based on different kmer length requirements. With each assembly, the number of total transcripts decreased while average contig length increased (see Additional file 1). A total of 2.3 billion reads representing different genotypes, treatments and time points were used in the assembly. The v4 assembly is a subset of the v3 assembly, with transcripts that were redundant, lacking open reading frames or expressed at low levels removed