SYNOPSIS
re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]
re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]
re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]]
re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]
DESCRIPTION
Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by performing STS and primer searches.
OPTIONS
- -p=hash-file
- Perform primer lookup using hash-file
- -P=hash-file
- Perform primer lookup using hash-file
- -s=hash-file
- Perform STS lookup using hash-file
- -S=hash-file
- Perform STS lookup using hash-file
- -n=mism
- Set max allowed mismatches per primer for lookup
- -g=gaps
- Set max allowed indels per primer for lookup
- -m=margin
- Set variability for STS size for lookup
- -l
- Use presize alignments (only if gaps>0)
- -G
- Print alignments in comments
- -d=min-max
- Set default STS size
- -r=+|-
- Enable/disable reverse STS lookup
- -O=+|-
- Enable/disable syscall optimisation
- -C=batchcnt
- Set number of STSes per batch
- -o=outfile
- Set output file name
- -q
-
Quiet (no progress indicator)
EXAMPLE
famap -tN -b genome.famap org/chr_*.fa
fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200
AUTHORS
This manual page was written by Andreas Tille <[email protected]> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.