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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 realigning 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 reliability profile, determine boundaries of the ncRNA. Compare to the flybase annotation and RNAz boundaries. perl v5.32.1 2022-11-19 LOCARNA...AZ-HITS(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS
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