./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/Haliotis_kam_transcriptome.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/Haliotis_midae_franchini -outfmt 10 -out /Volumes/Bay3/Dropbox/EIMD@FHL/Genomic_Data/anguilla/TEST -max_target_seqs 1 -num_threads 1


formatdb

./makeblastdb -in /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/RepBase_1707_invrep -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/RepBase_1707_invrep 

cd /Volumes/Bay3/software/ncbi-blast-2.2.26+/bin



Blasting v032 against RepBase1707_invrep….


RepBase_1707_invrep.fa

includes





./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/cgigas_alpha_v032.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/RepBase_1707_invrep -outfmt 10 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/cgigasv032_invREP_blastnout -task blastn -num_threads 2

cgigasv032_invREP_blastnout


 -outfmt <String>
   alignment view options:
     0 = pairwise,
     1 = query-anchored showing identities,
     2 = query-anchored no identities,
     3 = flat query-anchored, show identities,
     4 = flat query-anchored, no identities,
     5 = XML Blast output,
     6 = tabular,
     7 = tabular with comment lines,
     8 = Text ASN.1,
     9 = Binary ASN.1,
    10 = Comma-separated values,
    11 = BLAST archive format (ASN.1)

./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/cgigas_alpha_v032.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/RepBase_1707_invrep -outfmt 0 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/cgigasv032_invREP_blastnout_pairwise -task blastn -num_threads 4
cgigasv032_invREP_blastnout_pairwise


./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/cgigas_alpha_v032.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/RepBase_1707_invrep -outfmt 6 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/cgigasv032_invREP_blastnout_tab -task blastn -num_threads 4

cgigasv032_invREP_blastnout_tab