bio-ribo-seq-riboseq-preprocessing

Adapter Trimming

Goal: Remove 3' adapter sequences from ribosome footprint reads to recover the true insert.

Approach: Run cutadapt with the known adapter sequence and length filters to discard fragments outside the expected footprint range.

## Size Selection

**Goal:** Retain only reads corresponding to ribosome-protected fragments (typically 28-32 nt).

**Approach:** Apply minimum and maximum length filters with cutadapt to select the footprint size range.

```bash

## Typical: 28-32 nt (protected by ribosome)

cutadapt \
    -m 28 \
    -M 32 \
    -o size_selected.fastq.gz \
    trimmed.fastq.gz