Converts a list of PCR primer pairs to BED regions
Given a genomic FASTA file and a list of primers, this will generate a new
FASTA file for the targeted region. This targeted FASTA file can then be
used for targeted resequencing.
PCR input is expected to be paired FASTA entries with names like:
>primername/1
atatcgtgctacgatc
>primername/2
ttgatcggcatataaa
Tab-delimited input should be:
fwd-primer {tab} rev-primer
Uses http://genome.ucsc.edu/cgi-bin/hgPcr to perform ePCR.
Note: This operates by screen scraping, so it may break unexpectedly in the
future.
Usage: bedutils fromprimers {opts} -fasta file.fa
bedutils fromprimers {opts} -tab file.txt
bedutils fromprimers {opts} fwd_primer rev_primer
Options:
-db name DB to use
-perfect bases Minimum perfect bases (default: 15)
-good bases Minimum good bases (default: 15)
-size bases Max product size (default: 4000)
-flip Flip the reverse primer (default: False)