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#!/bin/bash -ve
export PERL_HASH_SEED=0
## generate alignment gff3 formatted output
../../util/gtf_to_alignment_gff3.pl stringtie_merged.gtf > stringtie_merged.gff3
## generate transcripts fasta file
# not including the genome here... too big, but here's how you'd do it.
#../../util/gtf_genome_to_cdna_fasta.pl stringtie_merged.gtf genome.fasta > stringtie_merged.transcripts.fasta
## Extract the long ORFs
../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S
## Predict likely ORFs
../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta $ARGS
## convert to genome coordinates
../../util/cdna_alignment_orf_to_genome_orf.pl stringtie_merged.transcripts.fasta.transdecoder.gff3 stringtie_merged.gff3 stringtie_merged.transcripts.fasta > stringtie_merged.transcripts.fasta.transdecoder.genome.gff3
## make bed files for viewing with GenomeView
# covert cufflinks gtf to bed
../../util/gtf_to_bed.pl stringtie_merged.gtf > stringtie_merged.bed
# convert the genome-based gene-gff3 file to bed
../../util/gff3_file_to_bed.pl stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 > stringtie_merged.transcripts.fasta.transdecoder.genome.bed
../../util/fasta_prot_checker.pl stringtie_merged.transcripts.fasta.transdecoder.pep
# Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\*
exit 0
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