-
Notifications
You must be signed in to change notification settings - Fork 0
Welcome to the Grass_annotation_pipeline wiki!
Amanda Hulse-Kemp edited this page Sep 28, 2022
·
2 revisions
Welcome to the Grass_annotation_pipeline wiki!
This pipeline is an attempt to develop a standardized method for annotating the grass genomes that we work with through the USDA-ARS Turfgrass consortium.
-
Mask Genome Run masking on SciNet @ CERES
-
Transfer Masked genome to @ATLAS
RNAseq data - QC?
Mapping reads - STAR, filtering?
Gene models with Trinity - Also on @CERES? Problematic right now on @ATLAS
- Run BRAKER2 on @ATLAS https://github.com/USDA-ARS-GBRU/Grass_annotation_pipeline/blob/main/runBraker.sh
- What evidence using for BRAKER2
MIKADO-BIND
-
Run EGGNog filtering on @ATLAS https://github.com/USDA-ARS-GBRU/Grass_annotation_pipeline/blob/main/runEggnog.sh
-
Run gFACs filtering on @ATLAS
-
Return to EGGNog output and filter out those removed from gFACs to retain soundly structured GFF3 file
Add figure from the flowchart we developed?