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Michael T. Wolfinger > Bio-ViennaNGS > splice_site_summary.pl

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NAME ^

splice_site_summary.pl - Find novel splice junctions in RNA-seq data.

SYNOPSIS ^

splice_site_summary.pl [-s FILE] [-a FILE] [-f FILE] [options]

DESCRIPTION ^

This program identifies and characterizes splice sites from mapped RNA-seq data against annotated splice junctions.

OPTIONS ^

-a

Reference annotation in BED12 format

-s

Splice junctions from mapped RNA-seq data in BED6 format

-f

Reference genome in Fasta format

-c

Chromosome sizes files

-b

Convert resuting BED6 files to bigBed format

-n

Filter canonical splice junctions

-i

Maximum intron length. Splice junctions covering introns larger than this value are not considered.

-r

Minimum read coverage for a splice junction. Only splice junctions that are supported by at least this number of reads are considered.

-w

Expand splice junctions by a window of this size on both sides

-o

Relative output path

-p

Prefix all output files with this string

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR ^

Michael T. Wolfinger <michael@wolfinger.eu>

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