Created
January 24, 2014 22:45
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these are the command line arguments to create a local blast database from the new genome assembly (in our case T. confusum), and then blast the large exon file to create what we will call a look up table.
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| # to construct database from an assembly in the file | |
| # conf.scaf.fa run this in the terminal | |
| # it will create a blast database call confscaf | |
| makeblastdb -in conf.scaf.fa -dbtype nucl -out confscaf | |
| # next we want to blast our large exons against this db | |
| blastn -query=/outputs/300+bpExons.fa -db=/blastDB/confscaf -outfmt='6 qseqid qstart sseqid sstart qlen length pident' -max_target_seqs=2 -out=info | |
| # this produces the lookup table that we can then use to analyze the degree of synteny conservation |
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