NAME

rnazIndex.pl - Convert data files as generated by rnazCluster.pl to different formats.

SYNOPSIS

 rnazIndex.pl [options] [file]

OPTIONS

-g, --gff

Generate GFF formatted output.

-b, --bed

Generate BED formatted output.

-c #:LABEL, --col #:LABEL

Append a column named LABEL to the HTML-table holding the data from the input file column with index #. e.g. rnazIndex.pl --html --col 19:Alifoldz --col 20:RNAmicro annotated.dat

-f, --fasta

Get sequences in FASTA format for loci or windows. See options --seq-dir, --forward, --reverse!

--seq-dir

Directory with sequence files. You only need this for FASTA output (see option --fasta). The files should be named with the sequence identifier and the extension .fa or .fasta. If your identifier in your input file is for example contig100 then you should have a file named contig100.fa. (If your identifier is of the form ``assembly.chromosome" as for example used by UCSC alignments, it is also possible to name the file chr22.fa for a sequence identifier hg17.chr22).

--forward, --reverse

Only relevant for FASTA output (see option --fasta). You can set if you want the forward or reverse complement of the sequence corresponding to a locus. Since loci don't have strand information you might consider both strands for further analysis. Windows have strand information, so if you export windows as FASTA these options are ignored.

--ucsc

In UCSC MAF alignment files it is common to use sequence identifiers like for example ``hg17.chr22". However, in BED are usually specific for a given assembly and therefore only ``chr22" is used in the BED files. With this option you change any identifier of the form ``X.Y" into ``Y". Moreover, the scores are multiplied by 1000 and rounded to integers since the UCSC genome browser expects scores between 0 and 1000.

-l, --loci

Use the locus information to generate the lines for the GFF and BED files. This is the default.

-w, --windows

Print the "windows" and not the "loci". Probably, rarely used function.

--html

With this option you get a HTML table which links to the the HTML pages which you can create by using the --html option in rnazCluster.pl. Redirect the output to some file which resides in the results directory created by rnazCluster.pl and open the file with your favourite web-browser.

-h, --help

Prints a short help message and exits.

--man

Prints a detailed manual page and exits.

DESCRIPTION

rnazIndex.pl reads tab-delimited data files as generated by rnazCluster.pl and converts them to GFF, BED or HTML formatted files.

GFF is the most widely used annotation file format and supported by many programs and systems (http://www.sanger.ac.uk/Software/formats/GFF).

BED is the native annotation file format used by the UCSC genome browser (http://genome.ucsc.edu).

EXAMPLES

 # rnazIndex.pl --gff results.dat > results.gff

Converts the results.dat file to GFF format.

 # rnazIndex.pl --ucsc --bed results.dat > results.bed

Create UCSC style BED format.

 # rnazIndex.pl --html results.dat > results/index.html

Generates HTML formatted table.

 # rnazIndex.pl --forward --fasta --seq-dir=seq results.dat

Exports sequences in FASTA format.

AUTHOR

Stefan Washietl <wash@tbi.univie.ac.at>