README.md

See overview and documentation:

Run MAKER

• To simplify handling of files, combine all the forward reads to one file and all the reverse reads to another.

cat *_1.fastq.gz >> forward_reads.fq.gz
cat *_2.fastq.gz >> reverse_reads.fq.gz

• Run trinity to predict transcripts and their potential proteins from RNA-Seq alignment:

  1. Run trinity for de novo transcriptome assembly:

     ./01_runTrinity.sh forward_reads.fq.gz reverse_reads.fq.gz

     Note: You will get the transcripts fasta file in trinity_run folder.

  2. Predict CDSs from transcriptome:

     ./02_runTransDecoder.sh trinity.fasta

     Note: You will get the protein sequence (trinity.fasta.transdecoder.pep) in working directory.

• Run maker by five steps:

  1. Generate the CTL files:

     module load GIF/maker
     module rm perl/5.22.1
     maker -CTL
     

     This will generate 3 CTL files (maker_opts.ctl, maker_bopts.ctl and maker_exe.ctl), you will need to edit them to make changes to the MAKER run. For the first round, change these lines in maker_opts.ctl file:

     genome=TAIR10_chr_all.fas
     est=trinity.fasta
     protein=trinity-swissprot-pep.fasta
     est2genome=1
     protein2genome=1
     TMP=/dev/shm
     

  2. Execute MAKER (03_maker_start.sh) in a slurm file. It is essential to request more than 1 node with multiple processors to run this efficiently.

     # Define a base name for maker output folder as the first argument.
     ./03_maker_start.sh maker_case
     

  3. Upon completion, train SNAP and AUGUSTUS:

     Use the same base name as previous step for first argument.
     ./04_maker_process.sh maker_case
     

  4. Train GeneMark with genome sequence:

     05_runGeneMark.sh TAIR10_chr_all.fas

  5. Once complete, modify the following lines in maker_opts.ctl file:

     snaphmm=maker.snap.hmm
     gmhmm=gmhmm.mod
     # Define a species as you want, but the name should not be existing in the augustus/config/species folder.
     augustus_species=maker_20171103
     

     Then, run (03_maker_start.sh) again:

     # Use the same base name as previous step for first argument.
     ./03_maker_start.sh maker_case
     

  6. Finalize predictions:

     06_maker_finalize.sh maker_case

     You will get the predicted gene models (maker_case.gff), protein sequences (maker_case.maker.proteins.fasta) and transcript sequence (maker_case.maker.transcripts.fasta) in the working directory.