abmapper Files

ABMapper is a software for spliced alignment and exonic alignment tool, written by C++ and PERL.

Requirement:
ABMapper binnary
runABMapper.pl
libabmapper.PL

Put these three files into same directory, and run: perl runABMapper.pl from the directory.


Platforms:
windows, linux, MacOSX

Currently, we just provide linux binary, the source codes and other platforms binary would be upload soon.

output file:
user can set -output in parameters, default is tmp-{sec}-{min}-{hour}-{mday}
*_tbl.txt: table file of all putative hits and fragments
*_pairinfo.txt: pair of fragments extended from two seeds
*.about: details pair infor with header
*.sam: SAM of fully matched reads
*.js.bed: bed file determined by canonical motif and distance limitation
{input}.repeat.fa: repeatitive reads which have more than {max_occurence} cutoff hits


About parameters:

1. '-overlap' value is important. most of reads could be over-extended, if there are no overlapping tolerance in spliced alignment
It will introduce high False Negative, however, if you set this value high, it would introduce False Positive.Generally, 8 is OK.

2. distance parameters: -min_dist and -max_dist. These two determine the searching range of two seeds hit. If you set it too high,
more results and high False Positive error would be introduced. Default is 10-400k

3. '-multi': maximum hits include exonic alignment and 'good' spliced alignment. If you set it too high, huge disk space was required.
Default is 400. If you set is 0, it would search all putative alignments.


Dev TEAM
18 July, 2010