Ab initio predictions
Pick one of the 2 ab initio prediction methods below:
Run BRAKER
Align RNA-Seq with splice aware aligner (STAR or HiSat2 preferred; HiSat2 used here)
Generate BAM file for each SRA-SRR id, merge them to generate a single sorted BAM file
Run BRAKER
Run MAKER
Align RNA-Seq with splice aware aligner (STAR or HiSat2 preferred; HiSat2 used here)
Generate BAM file for each SRA-SRR id, merge them to generate a single sorted BAM file
Run Trinity to generate transcriptome assembly using the BAM file
Run TransDecoder on Trinity transcripts to predict ORFs and translate them to protein
Run MAKER with transcripts (Trinity), proteins (TransDecoder and SwissProt), in homology-only mode
Use the MAKER predictions to train SNAP and AUGUSTUS. Self-train GeneMark
Run second round of MAKER with the above (SNAP, AUGUSTUS, and GeneMark) ab initio predictions plus the results from previous MAKER rounds.