Description

Expand a BED12 into a BED6 of in-frame mRNA positions, projected back to genomic coordinates. Default behaviour emits one row per codon (the 5' nucleotide); --step / --width / --frame control the stride, span and offset on the spliced mRNA. Useful for codon-level work on spliced features (e.g. ribo-seq P-site counts per codon, frame / periodicity QC, novel-ORF tiling).

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Tools

bed12codonpositions Documentation

Python helper that expands a BED12 into per-codon BED6 positions along the spliced feature, with configurable frame, step and span width via ext.args.

https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/bed12codonpositions/main.nfLicense: MIT
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