CLIPSeqTools::PreprocessApp::annotate_with_conservation - Annotate alignments in a database table with conservation scores.
clipseqtools-preprocess annotate_with_conservation [options/parameters]
Annotate alignments in a database table with phastCons or phyloP conservation scores. Adds a column named "conservation" with the average conservation score for the nucleotides of each read. To minimize storage needs, the conservation score is converted from floating point number to integer by multiplying with 1000.
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 --rname_sizes <Str> file with sizes for reference alignment sequences (rnames). Must be tab delimited (chromosome\tsize) with one line per rname. --cons_dir <Str> directory with phastCons or phyloP files. Database options. --drop drop column if it already exists (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.