CLIPSeqTools::PreprocessApp::annotate_with_genic_elements - Annotate alignments in a database table with genic information.
clipseqtools-preprocess annotate_with_genic_elements [options/parameters]
Annotate alignments in a database table with genic information Adds columns named "transcript", "exon", "coding_transcript", "utr5", "cds", "utr3". Column values will be NOT NULL if an alignment is contained in the corresponding region and NULL otherwise.
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. Database options. --drop drop columns if they already exist (not supported in SQlite). Other options. -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.