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riboseq-preprocessing

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Preprocess ribosome profiling reads with UMI handling, adapter trimming, contaminant/rRNA depletion, and footprint-aware alignment. Use when preparing Ribo-seq FASTQ for periodicity QC, ORF detection, translation efficiency, or stalling analysis, or when deciding how to deduplicate, which aligner to use, or how to size-select ribosome-protected fragments.

When to use

• UMI extraction
• adapter trimming
• contaminant/rRNA depletion
• footprint-aware alignment
• deduplication
• read-length distribution QC
• aligner selection
• ribosome-protected fragment size selection

When not to use

• periodicity QC
• ORF detection
• translation efficiency analysis
• stalling analysis

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