Table 1 Adjustable parameters for model scoring and read island assembly
Parameter | Default value |
|---|---|
Maximum homolog count | 3 |
Acceptable intron donor-acceptor pairs | GT-AG, GC-AG, AT-AC |
Minimum intron length | 10 |
Maximum intron length | 2000 |
Minimum protein length | 150 amino acids |
Low median coverage cutoff | 10 |
Low coverage penalty factor | 0.6 |
Acceptable range of exon coverage depth | 0.15 to 3 × transcript median depth |
Maximum length of low coverage run | 10 |
Low coverage run threshold | 0.05 × transcript mean depth |
Maximum N count per transcript | 8 |
Threshold score for “Matches RNA-Seq data” status | 0.5 |
Selection pseudoscore | 0.0001 |
Read island minimum cover depth | 3 |
Read island minimum length | 100 |