++ed by:
ZMUGHAL

1 PAUSE user

Emmanouil "Manolis" Maragkakis
and 1 contributors

NAME

CLIPSeqTools::App::count_reads_on_genic_elements - Count reads on transcripts, genes, exons, introns

SYNOPSIS

clipseqtools count_reads_on_genic_elements [options/parameters]

DESCRIPTION

Counts library reads on transcripts, genes, exons, introns.

* Transcript counts are measured only on their exons. * Gene counts are measured only for exonic regions.

Output (4 files): counts.gene.tab, counts.transcript.tab, counts.exon.tab, counts.intron.tab - (name, location, length, count, count_per_nt, exonic_count, exonic_length, exonic_count_per_nt)

OPTIONS

  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.
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message