cd ../data
curl -o Apul-genes.fasta https://gannet.fish.washington.edu/seashell/bu-github/deep-dive-expression/D-Apul/output/07-Apul-Hisat/genes.fastaApul epiMOD Annotation
Apul new genome
genes
https://gannet.fish.washington.edu/seashell/bu-github/deep-dive-expression/D-Apul/output/07-Apul-Hisat/genes.fasta
pulled via gff
head ../data/Apul-genes.fastamkdir ../output/25-Apul-epimods-blast/
/home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \
-in ../data/Apul-genes.fasta \
-dbtype nucl \
-out ../output/25-Apul-epimods-blast/Apul-genesfasta="../data/Machinery.fasta"
/home/shared/ncbi-blast-2.15.0+/bin/tblastn \
-query $fasta \
-db ../output/25-Apul-epimods-blast/Apul-genes \
-out ../output/25-Apul-epimods-blast/Mach-tblastn-Apul_out.tab \
-evalue 1E-05 \
-num_threads 48 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
2>/dev/nullwc -l ../output/25-Apul-epimods-blast/Mach-tblastn-Apul_out.tab446 ../output/25-Apul-epimods-blast/Mach-tblastn-Apul_out.tabhead ../output/25-Apul-epimods-blast/Mach-tblastn-Apul_out.tabDnmt1-201 mRNA::ptg000047l:7043865-7069644 83.544 79 13 0 1460 1538 22967 23203 1.51e-35 151
Dnmt3a-201 mRNA::ptg000016l:3572833-3602528 60.294 68 26 1 721 788 21872 22072 2.54e-13 77.0
Dnmt3b-201 mRNA::ptg000016l:3572833-3602528 77.273 44 10 0 817 860 29558 29689 3.88e-15 83.2
Dnmt3l-201 mRNA::ptg000035l:5201084-5245691 80.328 61 12 0 2124 2184 33195 33377 1.90e-22 109
USP9Y-201 mRNA::ptg000035l:5201084-5245691 80.328 61 12 0 1674 1734 33195 33377 1.36e-22 109
USP10-201 mRNA::ptg000025l:143698-155448 52.308 65 30 1 734 798 198 7 4.64e-11 69.3
USP11-201 mRNA::ptg000001l:4140337-4173729 70.000 130 39 0 306 435 20300 19911 2.92e-47 187
USP12-201 mRNA::ptg000018l:3278210-3285212 61.069 131 22 1 13 114 74 466 1.26e-42 161
USP14-201 mRNA::ptg000009l:1054171-1073449 69.643 56 15 1 1 54 92 259 1.86e-14 79.0
USP15-201 mRNA::ptg000001l:4140337-4173729 67.974 153 49 0 286 438 20300 19842 4.01e-59 224