preprocess_annotation

Collapse a multi-isoform GTF/GFF into simple per-gene models, optionally filtering isoforms by RNA-seq expression, so the later steps target one well-defined region per gene.

crisprware preprocess_annotation -g tests/test_data/ce11/chrIII_ce11.ncbiRefSeq.gtf \
  -m metagene consensus longest shortest

chrIII_ce11.ncbiRefSeq/
  chrIII_ce11.ncbiRefSeq_meta.gtf            # metagene: union of all exons
  chrIII_ce11.ncbiRefSeq_consensus.gtf       # exons shared by every isoform
  chrIII_ce11.ncbiRefSeq_longestCDS.gtf      # longest-CDS isoform per gene
  chrIII_ce11.ncbiRefSeq_shortestCDS.gtf     # shortest-CDS isoform per gene
  chrIII_ce11.ncbiRefSeq_genes_without_consensus_model.txt

Options you reach for

-m/--model metagene consensus longest shortest – which models to emit (any subset).
RNA-seq filter: -t/--tpm_files quant.sf ... (Salmon / Kallisto / FLAIR), then --median, --mean, --min, --max cutoffs, or -n/--top_n to keep the N highest-expressed isoforms per gene.
dCas targeting: --tss_window <up> <down> / --tes_window <up> <down> emit BED windows around the TSS / TES for CRISPRi/a.

Note

Feed the model you choose to generate_guides -k (restrict guides to it) and to rank_guides -t (group output per gene/transcript). Make sure the GTF and any TPM files share transcript IDs.