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LOCARNAP-REVISIT-RNAZ-HITS(1) User Contributed Perl Documentation LOCARNAP-REVISIT-RNAZ-HITS(1)

locarnap-revisit-RNAz-hits

locarnap-revisit-RNAz-hits [options]

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.

Brief help message
Full documentation
Extract all loci (in contrast, the default mode selects only loci that overlap with Flybase ncRNA annotation).
Special mode: draw n random instances
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.

2022-11-19 perl v5.32.1

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