List of good target binding primers

[marcomeola]

It would be great if the list of good target binding primers would be in the output even if there are 0 primer pairs passing non-target PCR check.

In the best case it would also be nice to get a table with how many and to which non-target species match the good target binding primers.

[biologger]

It is possible to get this information from the results of the primer QC step using MFEprimer.

• /primerdesign/{species_name}/Pangenome/results/primer/primerQC

  1) MFEprimer_template.csv (MFEprimer results for template DB) 2) MFEprimer_nontarget.csv (MFEprimer results for nontarget DB) 3) MFEprimer_assembly.csv (MFEprimer results for assembly DB)

In the results files the FpID and RpID are the ids of the primers (forward and reverse).

The HitID of the sequence in the database with a possible amplicon includes the database accession and the range taken from the original sequence (BLAST database) for the primer QC database.

Example: NZ_CADIKI010000002.1_85816_89816

More information about the sequence e.g. the sequence title can be extracted from the BLAST DB using blastdbcmd.

$ blastdbcmd -db /blastdb/ref_prok_rep_genomes -entry NZ_CADIKI010000002.1 -outfmt %t

[marcomeola]

Thank you!