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.