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

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NAME ^

normalize_multicov.pl - Compute normalized expression data from read counts

SYNOPSIS ^

normalize_multicov.pl [-i FILE] [-t RPKM|TPM] [--readlength INT] [options]

DESCRIPTION ^

This program computes normalized expression values in 'Transcript per Million' (TPM) or 'Reads per Megabase per Million' (RPKM) from read counts. The latter must be provided in the format produced by the 'bedtools multicov' utility, i.e. an extended BED12 file where each colum past the 12th lists read counts for one sample/condition.

OPTIONS ^

-i

Input file in 'bedtools multicov' output format, i.e. an extended BED12 file where each colum past the 12th lists the read counts for one sample/condition.

--readlength -r

Read length of the RNA-seq experiment.

--out -o

Output folder.

--type -t

Normalization method, either 'TPM' (default) or 'RPKM'.

--help -h

Print short help

--man

Prints the manual page and exits

SEE ALSO ^

TPM reference: Wagner et al, Theory Biosci. 131(4), pp 281-85 (2012)

AUTHOR ^

Michael T. Wolfinger <michael@wolfinger.eu>

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