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blast_protocol [2022/03/31 11:26] – 134.190.232.106blast_protocol [2022/09/06 14:49] (current) – 134.190.232.106
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 </code> </code>
  
-#This is another way to parse BLAST outputs via using -outfmt "6 qseqid sseqid ...+#This is another way to parse BLAST outputs via using -outfmt '6 qseqid sseqid ...' 
 <code> <code>
 #!/bin/bash #!/bin/bash
Line 97: Line 98:
 #$ -cwd #$ -cwd
 source activate blast source activate blast
-export BLASTDB=/db1/blastdb-sep1-2021/+export BLASTDB= /misc/scratch3/rogerlab_databases/other_dbs/nr_010621
 DB=nr DB=nr
 query=ATCG00670.1.fasta query=ATCG00670.1.fasta
-blastp -db $DB -query $query -out /scratch2/xizhang/BLASTP_nr.tsv -num_threads 2 -outfmt "6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle"+blastp -db $DB -query $query -out /scratch2/xizhang/BLASTP_nr.tsv -num_threads 2 -outfmt '6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle'
 source deactivate source deactivate
 </code> </code>
 +
 +Sep 6th,2022 Since Diamond is faster on BLASTP and BLASTx, this is another way using Diamond 
 +
 +<code>
 +#!/bin/bash
 +#$ -S /bin/bash
 +. /etc/profile
 +#$ -pe threaded 40
 +#$ -cwd
 +source activate /scratch2/software/anaconda/envs/diamond-2.0.7
 +#DB=nr
 +while read line
 +do 
 +
 +diamond blastp -p 40 -k 5 -e 1e-10 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle salltitles --header -d /misc/scratch3/rogerlab_databases/other_dbs/nr_02032022/diamond_nr.dmnd -q $line -o BLASTP_nr.$line.tsv --sensitive
 +
 +done <$1
 +
 +conda deactivate
 +
 +</code>
 +
  
 **V5 NCBI database** **V5 NCBI database**
blast_protocol.1648736796.txt.gz · Last modified: by 134.190.232.106