flatten-gtf

name	flatten-gtf
description	Use when you need to flatten exon-like GTF/GFF features into SAF meta-features for Subread or featureCounts workflows.
disable-model-invocation	true
user-invocable	true

flatten-gtf

Quick Start

• Command: flattenGTF -a <input.gtf> -o <output.saf>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/flattenGTF
• Full reference: See references/help.md

When To Use This Tool

• Convert GTF or GFF annotations into SAF for Subread-family tools.
• Flatten overlapping exon-like intervals into meta-features grouped by gene_id or another chosen attribute.
• Prepare annotation files for featureCounts workflows that prefer SAF over raw GTF/GFF parsing.

Common Patterns

# 1) Default flattening: exon features grouped by gene_id
/home/vimalinx/miniforge3/envs/bio/bin/flattenGTF \
  -a genes.gtf \
  -o genes.saf

# 2) Flatten a different feature type or grouping attribute
/home/vimalinx/miniforge3/envs/bio/bin/flattenGTF \
  -a annotation.gff3 \
  -o cds_by_tx.saf \
  -t CDS \
  -g transcript_id

# 3) Keep exon boundaries while still producing non-overlapping output
/home/vimalinx/miniforge3/envs/bio/bin/flattenGTF \
  -a genes.gtf \
  -o genes.keep_edges.saf \
  -C

Recommended Workflow

1. Start from an annotation built against the same assembly as your alignments.
2. Decide whether the defaults (-t exon, -g gene_id) match the downstream counting unit you want.
3. Write SAF to a new file with -o and inspect a few rows before large batch counting.
4. If merged intervals look too coarse, retry with -C to preserve exon edges.

Guardrails

• flattenGTF is the actual binary name; flatten-gtf is just the skill folder name.
• -a and -o are mandatory, and the tool writes SAF to disk rather than stdout.
• --help and --version are not standard GNU modes here; they print unrecognized option and then fall through to the usage banner.
• Defaults are -t exon and -g gene_id; if those attributes are absent the run will fail rather than guess.