normalize_multicov.pl - Compute normalized expression data from read counts
normalize_multicov.pl [-i FILE] [-t RPKM|TPM] [--readlength INT] [options]
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.
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.
Read length of the RNA-seq experiment.
Output folder.
Normalization method, either 'TPM' (default) or 'RPKM'.
Print short help
Prints the manual page and exits
TPM reference: Wagner et al, Theory Biosci. 131(4), pp 281-85 (2012)
Michael T. Wolfinger <michael@wolfinger.eu>
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ViennaNGS
CPAN shell
perl -MCPAN -e shell install Bio::ViennaNGS
For more information on module installation, please visit the detailed CPAN module installation guide.