CLIPSeqTools::App::distribution_on_genic_elements - Measure read distribution on 5'UTR, CDS and 3'UTR.
clipseqtools distribution_on_genic_elements [options/parameters]
Measure the distribution of reads along 5'UTR, CDS and 3'UTR. Will split the 5'UTR, CDS and 3'UTR of coding transcripts in bins and measure the read density in each bin. It will randomly keep a single transcript for each gene. The read copy number is not used in this analysis.
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 Other input --gtf <Str> GTF file with genes/transcripts. Output --o_prefix <Str> output path prefix. Script will create and add extension to path. [Default: ./] Other options. --bins <Int> number of bins each element is split into. [Default: 10] --length_thres <Int> genic elements shorter than this are skipped. [Default: 300] --plot call plotting script to create plots. -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.