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--- gene_prediction_just_augustus [2024/10/25 16:48] – 134.190.221.230
+++ gene_prediction_just_augustus [2024/10/28 10:17] (current) – 134.190.221.230
@@ Line 1: / Line 1: @@
-By Jason Shao & Joran Martijn (Last Edited: October 25th 2024)
+====== Gene prediction with just Augustus ======
+By Jason Shao & Joran Martijn (Last Edited: October 28th 2024)
 ====Intro====
@@ Line 8: / Line 9: @@
 source activate augustus-3.5.0
+# only required for species=generic
 export AUGUSTUS_CONFIG_PATH="/misc/scratch3/jasons/protist_gene_prediction/software/custom_augustus_config"
@@ Line 19: / Line 21: @@
 </code>
 Note that the species here is set to generic to minimize biases for a divergent organism. If your organism is closely related to one of the pre-trained species below, you can specify that instead to yield a better prediction.
+If you decide to use a pre-trained species, then you don't have to include the export line. The reason for including the export line is because augustus had stopped shipping probability files with generic species around 3.3.3. Why have they done that, you might ask? Well, unfortunately it's another great mystery for which science cannot explain.
 ====Pre-trained Species====
@@ Line 29: / Line 33: @@
 | tribolium                        | //Tribolium castaneum//                | Opisthokonta (Metazoa)       |
 | schistosoma                      | //Schistosoma mansoni//                | Opisthokonta (Metazoa)       |
-| tetrahymena                      | //Tetrahymena thermophila//            | SAR (Alveolata)              |
+| **tetrahymena**                      | **//Tetrahymena thermophila//**            | **SAR (Alveolata)**             |
 | galdieria                        | //Galdieria sulphuraria//              | Archaeplastida (Plantae)     |
 | maize                            | //Zea mays//                           | Archaeplastida (Plantae)     |
-| toxoplasma                       | //Toxoplasma gondii//                  | SAR (Alveolata)              |
+| **toxoplasma**                       | **//Toxoplasma gondii//**                  | **SAR (Alveolata)**              |
 | caenorhabditis                   | //Caenorhabditis elegans//             | Opisthokonta (Metazoa)       |
 | aspergillus_fumigatus            | //Aspergillus fumigatus//              | Opisthokonta (Fungi)         |