1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
|
## partition the genes
~/GITHUB/trinityrnaseq/util/misc/genome_gff3_to_gene_gff3_partitions.pl genes.gff3 genes.fa 500
find gene_contigs/ -regex ".*gene.fa" | tee fa_files.list
## simulate reads:
sim_reads.pl fa_files.list | tee sim.cmds
# Trinity
~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/run_trinity_no_LR.pl fa_files.list | tee trin.noFL.cmds
~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl ./fa_files.list | tee trin.withFL.cmds
# gmap the Trinity reconstructed transcripts to the gene sequence
find gene_contigs/ -regex ".*Trinity.fasta" > trin_fa.list
~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/gmap_to_ref.pl trin_fa.list > gmap.cmds
# cufflinks reconstruct
find gene_contigs/ -regex ".*genome.sam.coordSorted.bam" | tee bams.list
~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/bam_to_cuff.pl bams.list | tee cuff.cmds
# convert gff3 files to bed
find gene_contigs/ -regex ".*gene.gff3" | tee gene.gff3.list
~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl gene.gff3.list > gene.gff3.list.cmds
# convert cuff gtf to bed:
~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl cuff.list |tee cuff.list.cmds
########################################
# pull together all results for viewing.
find bin_0/ -regex '.*gene.gff3.bed' -exec cat {} \; | sort -k1,1 -k2,2n > all_genes.gff3.bed
find bin_0 -regex ".*trinity_WITH_LR_outdir.Trinity.fasta.gff3.bed" -exec cat {} \; | sort -k1,1 -k2,2n > trin.WITH_LR.bed
find bin_0 -regex ".*trinity_no_LR_outdir.Trinity.fasta.gff3.bed" -exec cat {} \; | sort -k1,1 -k2,2n > trin.no_LR.bed
find bin_0 -regex ".*transcripts.gtf.bed" -exec cat {} \; | sort -k1,1 -k2,2n > cuff_trans.bed
|
