CLIPSeqTools::App::nmer_enrichment_over_shuffled - Measure Nmer enrichment over shuffled reads.
clipseqtools nmer_enrichment_over_shuffled [options/parameters]
Measure words of length N (Nmer) enrichment and compare to shuffled reads. Shuffling is done at the nucleotide level and p-values are calculated using permutations.
Input options for library. --driver <Str> driver for database connection (eg. mysql, SQLite). --database <Str> database name or path to database file for file based databases (eg. SQLite). --table <Str> database table. --host <Str> hostname for database connection. --user <Str> username for database connection. --password <Str> password for database connection. --records_class <Str> type of records stored in database. --filter <Filter> filter library. May be used multiple times. Syntax: column_name="pattern" e.g. keep reads with deletions AND not repeat masked AND longer than 31 --filter deletion="def" --filter rmsk="undef" . --filter query_length=">31". Operators: >, >=, <, <=, =, !=, def, undef Output --o_prefix <Str> output path prefix. Script will create and add extension to path. [Default: ./] Other options. --nmer_length <Int> length N of the Nmer. Default: 6 --permutations <Int> number of permutation to be performed. Use more than 100 to get p-values < 0.01. --subset <Num> run analysis on random subset. Option specifies number (if integer) or percent (if % is used) of data to be used. -v --verbose print progress lines and extra information. -h -? --usage --help print help message
To install CLIPSeqTools, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CLIPSeqTools
CPAN shell
perl -MCPAN -e shell install CLIPSeqTools
For more information on module installation, please visit the detailed CPAN module installation guide.