Genomic intervals & annotation / Gene length calculation
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Effective length is the number of bases in the union of all exons of a gene across its transcripts: overlapping exons count once and introns are excluded. This is the usual gene length for computing TPM or FPKM from gene-level read counts.
The detailed table adds the number of merged exon blocks, the longest transcript, the gene span (introns included) and the length basis; bacterial annotations usually carry only CDS, so the union of CDS is used automatically.
The second chart shows effective length as a fraction of gene span: genes with many long introns have low values, single-exon genes are close to 1.
Download the two-column table and join it to a count matrix by gene ID; take care with duplicated names when joining by gene name.
Union-of-exons length (the definition of the Length column reported by featureCounts, Liao et al. 2014, Bioinformatics 30:923); cross-checked against an independent Python reference and per-gene sums from bedtools merge.
Runs in your browser; annotation files up to roughly 100 MB (about 300,000 lines) are recommended. For a complete human GTF (about 1.5 GB uncompressed), extract the chromosomes or genes you need first.
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