This script is used for high-througput anchoring of sequences in silico to physical map based on sequencing of 3-dimensional pools and Read mapping to sequences.
USAGE: $prog [OPTIONS]
EXAMPLE: $prog -mtp MTP_clones.txt -fpc 3DS.fpc -match End2End.txt -pool Pool_list.txt -cov Zipper_coverage/ -seq Sequence_list.txt -alp 75 -alc 3 -p Zipper_pct_75_cov_3
OPTIONS:
-h print this help
-mtp file with MTP address of each clone and corresponding address in BAC library
[MTP address] [BAC library address(in format used by FPC)]
------------------------------------------------------------
p01A01 TaaCsp3DS001A20
p01C11 TaaCsp3DS001B13
.... ...............
.... ...............
p10N20 TaaCsp3DS096P10
-fpc physical map *.fpc file
-match log file with matching clones from fpc
-pool file with pool list, each pool on separate line (pool names must correspond to MTP addresses in "mtp" file; plate pools must start with p, the number must reflect numbering of plates in MTP addresses; row pools must start with r followed by letter of row; column pools must start with c followed by two digits (if the mtp address if p03A12, corresponding pools should be p03, rA and c12)
-cov folder with coverage files, file name must be in format [pool_name]_coverage.txt (i.e. c05_coverage.txt for column pool c05; name must be same with pool name in "pool" file)
-seq file with marker list (same names as in coverage files)
-alp alignment percentage threshold (default 80)
-p prefix of output file