Genomic intervals & annotation / Gene length calculation
Your data stays in your browser: files are read and processed on your device, never uploaded to any server, and cleared when you close the page. Free, no sign-in.
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.
Bioinformatics services are provided by HST GENOMICS. Analysis first, pay later. Not satisfied? You pay nothing.