High nucleotide sensitivity/specificity, zero gene level
Posted: Thu Nov 19, 2015 7:43 pm
Originally posted in the old forum by AB on 27.08.2014 - 00:22
sensitivity/specificity poor on gene level
Hi there,
I am trying to train Augustus on the beet genome because this is the closest related reference genome to my plant. But, I think I am doing something wrong. The results to training with first 100 random genes, then 1000 random genes, have yielded high nucleotide level sensitivity (0.936) and specificity (0.823), low values for exon level (0.394 sensitivity, 0.345 specificity), but 0 for the gene level. Does anyone have any suggestions?
sensitivity/specificity poor on gene level
Hi there,
I am trying to train Augustus on the beet genome because this is the closest related reference genome to my plant. But, I think I am doing something wrong. The results to training with first 100 random genes, then 1000 random genes, have yielded high nucleotide level sensitivity (0.936) and specificity (0.823), low values for exon level (0.394 sensitivity, 0.345 specificity), but 0 for the gene level. Does anyone have any suggestions?
Code: Select all
genes.gb:5149
genes.gb.test:1000
genes.gb.train:4149
Evaluation of gene prediction *******
| sensitivity | specificity |
|
nucleotide level | 0.936 | 0.823 |
/
| #pred | #anno | | FP = false pos. | FN = false neg. | | |
| total/ | total/ | TP |--------------------|--------------------| sensitivity | specificity |
| unique | unique | | part | ovlp | wrng | part | ovlp | wrng | | |
|
| | | | 1620 | 1310 | | |
exon level | 2473 | 2163 | 853 | ------------------ | ------------------ | 0.394 | 0.345 |
| 2473 | 2163 | | 777 | 234 | 609 | 781 | 282 | 247 | | |
/
transcript | #pred | #anno | TP | FP | FN | sensitivity | specificity |
|
gene level | 735 | 560 | 0 | 735 | 560 | 0 | 0 |
/