Differences

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--- blast_protocol [2022/09/06 14:07] – 134.190.232.106
+++ blast_protocol [2022/09/06 14:49] (current) – 134.190.232.106
@@ Line 89: / Line 89: @@
 </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>
@@ Line 101: / Line 101: @@
 DB=nr
 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
 </code>
@@ Line 118: / Line 118: @@
 do
-diamond blastp -d /misc/scratch3/rogerlab_databases/other_dbs/nr_02032022/diamond_nr.dmnd -q $line -o Diamond_nr.$line.tsv --very-sensitive
+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