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LOCARNA...AZ-HITS(1)   User Contributed Perl Documentation  LOCARNA...AZ-HITS(1)

NAME
     locarnap-revisit-RNAz-hits

SYNOPSIS
     locarnap-revisit-RNAz-hits [options]

DESCRIPTION
     Revisits  the  hits  of the fly RNAz screen and prepares input data for re-
     aligning all loci with locarnap-realign-all.pl. The script is usually  used
     as first step in a pipeline for refining RNAz hits with LocARNA-P.

OPTIONS
     --help
	 Brief help message

     --man
	 Full documentation

     --all
	 Extract  all loci (in contrast, the default mode selects only loci that
	 overlap with Flybase ncRNA annotation).

     --random <n>
	 Special mode: draw n random instances

     --context <c>
	 Extract with maximal context of c columns upstream and downstream.

     In default mode, determine the RNAz hits with dmel flybase  annotation.  In
     random  mode, draw n random hits. With flag --all select all hits.  For the
     selected hits get the annotation and the position in the  pecan  alignment.
     Determine	the sequences that are well-aligned to the dmel sequence, obtain
     these sequences with genomic context (option --context, default=100).

     Goal: use these sequence for realining by locarna. From the locarna  relia-
     bility  profile,  determine boundaries of the ncRNA. Compare to the flybase
     annotation and RNAz boundaries.

perl v5.38.2			   2022-10-04		    LOCARNA...AZ-HITS(1)

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<https://man.freebsd.org/cgi/man.cgi?query=locarnap-revisit-RNAz-hits.pl&sektion=1&manpath=FreeBSD+Ports+15.1.quarterly>

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