42 lines
1.7 KiB
Plaintext
42 lines
1.7 KiB
Plaintext
## partition the genes
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~/GITHUB/trinityrnaseq/util/misc/genome_gff3_to_gene_gff3_partitions.pl genes.gff3 genes.fa 500
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find gene_contigs/ -regex ".*gene.fa" | tee fa_files.list
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## simulate reads:
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sim_reads.pl fa_files.list | tee sim.cmds
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# Trinity
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~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/run_trinity_no_LR.pl fa_files.list | tee trin.noFL.cmds
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~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl ./fa_files.list | tee trin.withFL.cmds
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# gmap the Trinity reconstructed transcripts to the gene sequence
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find gene_contigs/ -regex ".*Trinity.fasta" > trin_fa.list
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~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/gmap_to_ref.pl trin_fa.list > gmap.cmds
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# cufflinks reconstruct
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find gene_contigs/ -regex ".*genome.sam.coordSorted.bam" | tee bams.list
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~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/bam_to_cuff.pl bams.list | tee cuff.cmds
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# convert gff3 files to bed
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find gene_contigs/ -regex ".*gene.gff3" | tee gene.gff3.list
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~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl gene.gff3.list > gene.gff3.list.cmds
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# convert cuff gtf to bed:
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~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl cuff.list |tee cuff.list.cmds
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########################################
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# pull together all results for viewing.
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find bin_0/ -regex '.*gene.gff3.bed' -exec cat {} \; | sort -k1,1 -k2,2n > all_genes.gff3.bed
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find bin_0 -regex ".*trinity_WITH_LR_outdir.Trinity.fasta.gff3.bed" -exec cat {} \; | sort -k1,1 -k2,2n > trin.WITH_LR.bed
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find bin_0 -regex ".*trinity_no_LR_outdir.Trinity.fasta.gff3.bed" -exec cat {} \; | sort -k1,1 -k2,2n > trin.no_LR.bed
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find bin_0 -regex ".*transcripts.gtf.bed" -exec cat {} \; | sort -k1,1 -k2,2n > cuff_trans.bed
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