GenomeComb

Primercheck

Format

cg primercheck ?options? primerfile dbdir ?resultfile?

Summary

check primer sets for multiple amplicons and snps

Description

This command checks a list of primersets, given in a tab separated file with at least the columns name, primer1, primer2. It will add the location of the amplicon amplified by these primers (in the genome given in dbdir) as columns chromosome, begin, end. If the full primers match more than one amplicon, these values cannot be attributed.

The command will also perform an ePCR by checking if the 15base end parts of the primers amplify more than 1 amplicon; the number of amplicons found is in the column "numamplicons", the location of the amplicons in "amplicons".

The positions of the primers are checked for known snps (in dbsnp). All snps found are listed in the columns "primer1_snps" and /"primer2_snps", together with information about position,frequency and validation status. The frequency of the most frequent snp is shown in columns "primer1_snpsmaxfreq" and "primer2_snpsmaxfreq".

The "amplicon_fts" column will list any homopolymers detected in the amplicon.

Arguments

primerfile
tsv file that has at least the columns name, primer1, primer2
dbdir
directory containing reference genomes and variation data
resultfile
results will be written to this file if given, otherwise to stdout

Options

-m maxnum
further analysis stops if a primer has > maxnum hits in the genome (default 5000)
-s maxsize
only amplicons smaller than maxsize are considered in numamplicons (default 1000)
-a maxamplicons
if more than maxamplicons are found, further analysis is aborted (default 100)

Category

Validation