rnazMAF2BED.pl
- Convert sequence information from MAF formatted
multiple sequence alignment to a BED style annotation format.
rnazMAF2BED.pl [options] [file]
Specify the sequence identifier of the sequence which should be used
as a reference to create the output. Use for example hg17
if you
want to get all sequences containing hg17
in the idenitfier
(e.g. hg17.chr10
, hg17.chr22
,...). If this option is omitted,
the first sequence identifier of the first sequence in the first
alignment block is used.
Combine overlapping alignments and report non-overlapping regions in the BED output.
Prints version information and exits.
Prints a short help message and exits.
Prints a detailed manual page and exits.
This simple programs extracts the position information for a given sequence out of a MAF alignment and outputs it in a BED style annotation format.
# rnazMAF2BED.pl -s hg17 some.maf
Get the regions of the hg17 sequences in the alignment some.maf
.
Stefan Washietl <wash@tbi.univie.ac.at>