Table 1.
Numbers of clones and clusters affected by novel solutions to the pipeline. These numbers relate to the total of 19,107 clones selected from 26,186 gene clusters and 9380 singletons covering 9083 KH2012 protein coding genes.
| Novel solution | Step affected | Entity affected | Numbers | Comments |
|---|---|---|---|---|
| Opposite strand splitting | Gene clustering | Cluster | +476 | Each split cluster may provide full-ORF clones |
| Cliff score | 5′ end detection | Cluster | +3687 | May not be the only evidence used to assess that cluster is full-ORF |
| SL trans-splicing | 5′ end detection | Clone | +5049 | All SL read containing cluster are considered to have the 5′ end fo the ORF, irrespective of cliff score |
| Alternative transcripts | Non-redundant clone selection | Clone | +449 | Additional clones selected in case of alternative transcripts |
| Exon mapping analysis | Final clone list | Clone | −5000 | Excessive number of clones mapping to same locus with same exon structure |
| Manual addition of clones | Final clone list | Clone | +37 | Clones for low abundanec developmental genes with known ORF |