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get protospacers

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nyoungb2 edited this page Nov 5, 2013 · 4 revisions

This is a workflow for getting protospacers from a spacer blast table

See spacer blast if you have not yet performed the spacer BLAST
Your blast table must be in the output format: '7 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen btop'
blastdbcmd will be used to pull out the protospacers from the blast database of interest. The comment lines in the blast table will specify the blast database.
The full length protospacers and protospacers + 5'/3' extensions (default of 10bp) will be appended as new columns to the blast table.

CLdb_spacerBlastGetProto.pl < spacer_groups_filtered_blast.txt > spacer_groups_filt_proto_blast.txt

for more information on the output:

perldoc CLdb_spacerBlastGetProto.pl

write out a fasta of the protospacers

CLdb_spacerBlastGetProto.pl < spacer_groups_filt_proto_blast.txt > spacer_groups_filt_proto_blast.fasta