!head /Volumes/Bay4\ scratch/oyster.v9.glean.final.rename.gff !wc /Volumes/Bay4\ scratch/oyster.v9.glean.final.rename.gff #not quite a GFF! !head /Volumes/Bay4\ scratch/oyster.v9.glean.final.rename.gff.pep #not quite a GFF! !head /Volumes/Bay4\ scratch/oyster.v9.glean.final.rename.gff.CDS !head /Volumes/web/cnidarian/oyster.v9.glean.final.rename.CDS.gff !head /Volumes/web/cnidarian/oyster.v9.glean.final.rename.mRNA.gff !wc /Volumes/web/cnidarian/oyster.v9.glean.final.rename.CDS.gff !wc /Volumes/web/cnidarian/oyster.v9.glean.final.rename.mRNA.gff #check to make sure files add up. sum(196691 + 28027) cp /Volumes/web/cnidarian/oyster.v9.glean.final.rename.CDS.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff cp /Volumes/web/cnidarian/oyster.v9.glean.final.rename.mRNA.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff !wc /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff !fgrep -c "fuzznuc nucleotide_motif" /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff !head /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff cp /Volumes/web/cnidarian/TJGR_oyster_v9_CG.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff !sortbed -i /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff > /Volumes/web/cnidarian/TJGR_oyster_v9_CG_sorted.gff !wc /Volumes/web/cnidarian/TJGR_oyster_v9_CG_sorted.gff !head /Volumes/web/cnidarian/qDOD_scaffold_length.csv !tr ',' "\t" /Volumes/web/cnidarian/qDOD_scaffold_length.txt !head /Volumes/web/cnidarian/qDOD_scaffold_length.txt !flankbed -s -l 1000 -r 0 -i /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff -g /Volumes/web/cnidarian/qDOD_scaffold_length.txt > /Volumes/web/cnidarian/TJGR_Promoter_1k5p.gff !head /Volumes/web/cnidarian/TJGR_Promoter_1k5p.gff !sed 's/mRNA/promoter/g' /Volumes/web/cnidarian/TJGR_Promoter_1k5p_b.gff !head /Volumes/web/cnidarian/TJGR_Promoter_1k5p_b.gff http://eagle.fish.washington.edu/cnidarian/TJGR_Promoter_1k5p_b.gff cp /Volumes/web/cnidarian/TJGR_Promoter_1k5p_b.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff #clean up in SQLShare !head /Volumes/web/cnidarian/Cgigas_v9_1k5p_gene_promoter_v2.gff !tail -n +2 /Volumes/web/cnidarian/Cgigas_v9_1k5p_gene_promoter_v2.gff > /Volumes/web/cnidarian/Cgigas_v9_1k5p_gene_promoter_v2b.gff !tr ',' "\t" /Volumes/web/cnidarian/Cgigas_v9_1k5p_gene_promoter_v2c.gff !head /Volumes/web/cnidarian/Cgigas_v9_1k5p_gene_promoter_v2c.gff !cp /Volumes/web/cnidarian/Cgigas_v9_1k5p_gene_promoter_v2c.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff !sed 's/Parent=/#Parent=/g' /Volumes/web/cnidarian/TJGR_Cgigas_v9_exon_b.gff !sed 's/ID=/#ID=/g' /Volumes/web/cnidarian/TJGR_Cgigas_v9_gene_b.gff !head /Volumes/web/cnidarian/TJGR_Cgigas_v9_exon_b.gff !subtractBed -a /Volumes/web/cnidarian/TJGR_Cgigas_v9_gene_b.gff -b /Volumes/web/cnidarian/TJGR_Cgigas_v9_exon_b.gff > /Volumes/web/cnidarian/Cgigas_v9_intron.gff !head /Volumes/web/cnidarian/Cgigas_v9_intron.gff !sed 's/#ID=/Parent=/g' /Volumes/web/cnidarian/Cgigas_v9_intron_b.gff !sed 's/GLEAN/subtractBed/g' /Volumes/web/cnidarian/Cgigas_v9_intron_c.gff !sed 's/mRNA/_intron/g' /Volumes/web/cnidarian/Cgigas_v9_intron_d.gff !head /Volumes/web/cnidarian/Cgigas_v9_intron_d.gff http://eagle.fish.washington.edu/cnidarian/Cgigas_v9_intron_d.gff cp /Volumes/web/cnidarian/Cgigas_v9_intron_d.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff #will clean up in SQLSHARE !head /Volumes/web/cnidarian/Cgigas_v9_intron_v2d.gff #!tail -n +2 /Volumes/web/cnidarian/Cgigas_v9_intron_v2b.gff > /Volumes/web/cnidarian/Cgigas_v9_intron_v2c.gff !sed 's/intron/intrn/g' /Volumes/web/cnidarian/Cgigas_v9_intron_v2d.gff cp /Volumes/web/cnidarian/Cgigas_v9_intron_v2d.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff !wc /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff !wc /Volumes/web/cnidarian/Cgigas_v9_intron_d.gff !complementBed -i /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff -g /Volumes/web/cnidarian/qDOD_scaffold_length.txt > /Volumes/web/cnidarian/TJGR_complement_exon.bed !head /Volumes/web/cnidarian/TJGR_complement_exon.bed !intersectBed -a /Volumes/web/cnidarian/TJGR_complement_exon.bed -b /Volumes/web/cnidarian/TJGR_Cgigas_v9_gene_b.gff > /Volumes/web/cnidarian/TJGR_intron2.bed !head /Volumes/web/cnidarian/TJGR_intron2.bed !head /Volumes/web/bivalvia/wholegenomefiles_MBDbsSeq_gill/gffs/qDOD_RepeatProteinMask_v9_asgff.gff cp /Volumes/web/bivalvia/wholegenomefiles_MBDbsSeq_gill/gffs/qDOD_RepeatProteinMask_v9_asgff.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff $ cat file1 file2 ... fileN > file1-N.nonunique.bed $ mergeBed -i file1-N.nonunique.bed > file1-N.merged.bed !cat /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff > /Volumes/web/cnidarian/TJGR_gene_TE_promoter.gff !head /Volumes/web/cnidarian/TJGR_gene_TE_promoter.gff !sortBed -i /Volumes/web/cnidarian/TJGR_gene_TE_promoter.gff > /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s.gff !head /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s.gff !mergebed -i /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s.gff > /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s_unique.bed !head /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s_unique.bed !complementBed -i /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s_unique.bed -g /Volumes/web/cnidarian/qDOD_scaffold_length.txt > /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s_unique_comp.bed !head /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s_unique_comp.bed http://eagle.fish.washington.edu/cnidarian/TJGR_gene_TE_promoter_s_unique_comp.bed cp /Volumes/web/cnidarian/TJGR_gene_TE_promoter_s_unique_comp.bed /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed !cat /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web/cnidarian/TJGR_CanTest !head /Volumes/web/cnidarian/TJGR_CanTest !sortBed -i /Volumes/web/cnidarian/TJGR_CanTest > /Volumes/web/cnidarian/TJGR_CanTest_s !mergebed -i /Volumes/web/cnidarian/TJGR_CanTest_s > /Volumes/web/cnidarian/TJGR_CanTest_s_unique.bed !head /Volumes/web/cnidarian/TJGR_CanTest_s_unique.bed http://eagle.fish.washington.edu/cnidarian/TJGR_CanTest_s_unique.bed !intersectBed -a /Volumes/web/cnidarian/TJGR_CanTest_s_unique.bed -b /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web/cnidarian/TJGR_CanTest_s_unique_inter_COMP.bed !wc /Volumes/web/cnidarian/TJGR_CanTest_s_unique_inter_COMP.bed !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed !head /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff IGV session file available: http://eagle.fish.washington.edu/cnidarian/oyster_v9_igv_session.xml !head /Volumes/web/cnidarian/BiGill_meth_v9_5x.igv