OkORF

Predict ORFs in transcriptome sequences, e.g. RNA-seq de novo assembly.

OkORF is a sort of modification of TransDecoder by B. Haas. Many codes of TransDecoder are borrowed.

How to use?

$ cp OkORF/run.conf.yml.example ./run.conf.yml
$ cp OkORF/run.rb ./

edit run.conf.yml

$ ruby run.rb

6 shell scripts are generated.

submit scripts to SGE by running sge_submit_Mcra_131016p3.sh.

sge_submit_Mcra_131016p3.sh

Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
PerlLib		PerlLib
util		util
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
VERSION		VERSION
capture_all_ORFs.pl		capture_all_ORFs.pl
get_fasta_entries_from_idlist.rb		get_fasta_entries_from_idlist.rb
get_gff_entries_from_idlist.rb		get_gff_entries_from_idlist.rb
orf_prediction.rb		orf_prediction.rb
orf_prediction_step1_find_goodORFs_for_training.rb		orf_prediction_step1_find_goodORFs_for_training.rb
orf_prediction_step2_BLASTPref.rb		orf_prediction_step2_BLASTPref.rb
orf_prediction_step3_buildTrainSeq.rb		orf_prediction_step3_buildTrainSeq.rb
orf_prediction_step4_ORFPredict_round2.rb		orf_prediction_step4_ORFPredict_round2.rb
orf_prediction_step5_rescueGM_prep.rb		orf_prediction_step5_rescueGM_prep.rb
orf_prediction_stepN_rescueGM_from_BLAST_Pfam.rb		orf_prediction_stepN_rescueGM_from_BLAST_Pfam.rb
orf_prediction_stepZ_merge_finalize.rb		orf_prediction_stepZ_merge_finalize.rb
pfam_runner.pl		pfam_runner.pl
remove_duplicates_in_fastaf.rb		remove_duplicates_in_fastaf.rb
run.conf.yml.example		run.conf.yml.example
run.conf.yml.example2		run.conf.yml.example2
run.rb		run.rb
run_blastp.sh		run_blastp.sh
run_cdhit_cds_global.sh		run_cdhit_cds_global.sh
run_cdhit_cds_local_p2.sh		run_cdhit_cds_local_p2.sh
select_good_orfs_based_on_markovscore_and_length.rb		select_good_orfs_based_on_markovscore_and_length.rb
select_train_models_based_on_blastp_results.rb		select_train_models_based_on_blastp_results.rb