#Contigs from Assembly
!head /Volumes/web/cnidarian/SeaStar_transc_v2.fa
>3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)_contig_1 CAAATATATGAACGGTTGATTGTCAACGATTAGTACATGTTTTCATTGTTCCCCACGCCC GCCCCCCCCCACTCAAACATTTAAAGTGTGAAATATTATTTATCCACAAATTTCCTTAAA CCTGCAAACTTGTCTGCTGTCTCTTATTGGAAGTTATGAAAAAGAACAACGGGTTTTCTT TAAAGGGTCTGCGTGCGATTTTCAACCTTTTGAGTAATAGCAGTTATTTTGATAACCGAT TTTTTTCAAAGCTCAACAGCTTTTTAAAATAAGGAATCCTATAATGGCCAAACGAATACT ATAAAAATAAGGGTTCTCTTAATTGTATAAAACGTATAATTTTATCAATTTTGGGACCGT GTAATTTTTTAAAGACCACAAGAATGTTACATACAACAAATAGACGAAACTCGTAGCTTT GGAAACTACGTCATGGGCGTTTGGTCAAAAGCTGGAGAGAAAGAGAGGTGGGGTGCCAGA CTTAAGTAGTCACGTGATCTGACCAACGCACATCGGAAGCTCGATCGGATGAAATCTTCT
#Making the query look better
!sed 's/3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)/Phel_clc/g' </Volumes/web/cnidarian/SeaStar_transc_v2.fa> /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa
!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa
>Phel_clc_contig_1 CAAATATATGAACGGTTGATTGTCAACGATTAGTACATGTTTTCATTGTTCCCCACGCCC GCCCCCCCCCACTCAAACATTTAAAGTGTGAAATATTATTTATCCACAAATTTCCTTAAA CCTGCAAACTTGTCTGCTGTCTCTTATTGGAAGTTATGAAAAAGAACAACGGGTTTTCTT TAAAGGGTCTGCGTGCGATTTTCAACCTTTTGAGTAATAGCAGTTATTTTGATAACCGAT TTTTTTCAAAGCTCAACAGCTTTTTAAAATAAGGAATCCTATAATGGCCAAACGAATACT ATAAAAATAAGGGTTCTCTTAATTGTATAAAACGTATAATTTTATCAATTTTGGGACCGT GTAATTTTTTAAAGACCACAAGAATGTTACATACAACAAATAGACGAAACTCGTAGCTTT GGAAACTACGTCATGGGCGTTTGGTCAAAAGCTGGAGAGAAAGAGAGGTGGGGTGCCAGA CTTAAGTAGTCACGTGATCTGACCAACGCACATCGGAAGCTCGATCGGATGAAATCTTCT
!fgrep -c ">" /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa
30578
#IMPORTANT the location of files will change depending on your computer
!blastx \
-query /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa \
-db /Users/Shared/data/blast/db/uniprot_sprot \
-out /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_1.tab \
-outfmt 6 \
-num_threads 8 \
-max_hsps 1 \
-max_target_seqs 1 \
-evalue 1E-20
!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_1.tab
Phel_clc_contig_4 sp|P25001|COX1_PISOC 88.39 517 48 1 7061 5547 1 517 0.0 749 Phel_clc_contig_7 sp|Q33818|CYB_ASTPE 79.94 329 66 0 993 7 51 379 9e-168 479 Phel_clc_contig_8 sp|P68037|UB2L3_MOUSE 76.97 152 35 0 4862 4407 1 152 7e-62 214 Phel_clc_contig_9 sp|Q0MVN8|QOR_PIG 45.61 239 129 1 796 80 90 327 5e-63 210 Phel_clc_contig_17 sp|Q6DGL8|RT15_DANRE 35.00 180 107 3 1177 638 61 230 5e-22 99.8 Phel_clc_contig_18 sp|P96202|PPSC_MYCTU 30.81 714 438 15 5407 3386 1414 2111 6e-76 286 Phel_clc_contig_20 sp|P46058|EDSP_CYNPY 31.03 348 218 8 1731 703 4 334 5e-38 148 Phel_clc_contig_22 sp|Q96LI5|CNO6L_HUMAN 60.78 357 128 5 1887 832 186 535 2e-149 450 Phel_clc_contig_24 sp|P63245|GBLP_RAT 80.77 312 60 0 1032 97 1 312 0.0 540 Phel_clc_contig_25 sp|Q9QYP1|LRP4_RAT 32.74 623 393 7 1816 5 393 1008 1e-99 339
!tr '|' "\t" </Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_1.tab> /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_sqlready.tab
!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_sqlready.tab
Phel_clc_contig_4 sp P25001 COX1_PISOC 88.39 517 48 1 7061 5547 1 517 0.0 749 Phel_clc_contig_7 sp Q33818 CYB_ASTPE 79.94 329 66 0 993 7 51 379 9e-168 479 Phel_clc_contig_8 sp P68037 UB2L3_MOUSE 76.97 152 35 0 4862 4407 1 152 7e-62 214 Phel_clc_contig_9 sp Q0MVN8 QOR_PIG 45.61 239 129 1 796 80 90 327 5e-63 210 Phel_clc_contig_17 sp Q6DGL8 RT15_DANRE 35.00 180 107 3 1177 638 61 230 5e-22 99.8 Phel_clc_contig_18 sp P96202 PPSC_MYCTU 30.81 714 438 15 5407 3386 1414 2111 6e-76 286 Phel_clc_contig_20 sp P46058 EDSP_CYNPY 31.03 348 218 8 1731 703 4 334 5e-38 148 Phel_clc_contig_22 sp Q96LI5 CNO6L_HUMAN 60.78 357 128 5 1887 832 186 535 2e-149 450 Phel_clc_contig_24 sp P63245 GBLP_RAT 80.77 312 60 0 1032 97 1 312 0.0 540 Phel_clc_contig_25 sp Q9QYP1 LRP4_RAT 32.74 623 393 7 1816 5 393 1008 1e-99 339