Table 1.
Contig retention through the screening pipeline for novel lncRNAs
| Step | % Contigs Eliminated | # Contigs Eliminated | # Contigs Remaining |
|---|---|---|---|
| Orthology analysis (BLASTn) | 62.7 | 54,405 (a) | 32,309 novel |
| Probable noncoding (CPAT p < 0.01) | 70.1 | 22,781 | 9528 |
|
High confidence noncoding (CPAT q < 0.01) |
98.1 | 9346 | 182 |
| Pfam annotations | 0 | 0 | 182 |
| align to genome and compare to MAKER annotations | 19.2 | 35 | 147 |
Columns as follows: “Step”, the name of the program or step in the screening pipeline; “% Contigs Eliminated”, the percentage of contigs from Column 4 of the previous row in the table that were eliminated in this step of the analysis pipeline; “# Contigs Eliminated”, the number of contigs corresponding to the percentage in Column 2; “# Contigs Remaining”, the number of contigs remaining after the row’s filtering Step was applied. The number of starting contigs before step 1 (“Orthology analysis”) was 86,714
(a) This includes the 40 beaver contigs that we identified that are orthologs of known noncoding transcripts in other species (Fig. 9, purple rectangle). The percentage shown in column “% Contigs Eliminated” is for that specific step (row) relative to the number of contigs before that step.