GTFtools: a software package for analyzing various features of gene models

Abstract

Motivation Gene-centric bioinformatics studies frequently involve calculation or extraction of various features of genes such as splice sites, promoters, independent introns, and untranslated regions (UTRs) through manipulation of gene models. Gene models are often annotated in gene transfer format (GTF) files. The features are essential for subsequent analysis such as intron retention detection, DNA-binding site identification, and computing splicing strength of splice sites. Some features such as independent introns and splice sites are not provided in existing resources including the commonly used BioMart database. A package that implements and integrates functions to analyze various features of genes will greatly ease routine analysis for related bioinformatics studies. However, to the best of our knowledge, such a package is not available yet. Results In this work, we introduce GTFtools, a stand-alone command-line software that provides a set of functions to calculate various gene features, including splice sites, independent introns, transcription start sites (TSS)-flanking regions, UTRs, isoform coordination and length, different types of gene lengths, etc. It takes the ENSEMBL or GENCODE GTF files as input, and can be applied to both human and non-human gene models like the lab mouse. We compare the utilities of GTFtools with those of two related tools: Bedtools and BioMart. GTFtools is implemented in Python and not dependent on any third-party software, making it very easy to install and use. Availability GTFtools is freely available at www.genemine.org/gtftools.php as well as pyPI and Bioconda

A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome

“…2014 ), and then aligned sequences to GRCz11 as above. We used GTFtools ( Li et al . 2022 ) to analyze Ens92 gene models and used the length of merged exons of isoforms of each gene to calculate TPM (transcripts per kilobase of gene length per million total reads) for all protein-coding genes in each library.…”

A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome

“…These libraries did not have molecular barcodes, so we removed the adapters with Cutadapt (Martin 2011), quality trimmed with Trimmomatic (Bolger et al 2014), and then aligned to GRCz11 as above. We used GTFtools (Li et al 2022) to analyze Ens92 gene models and used the length of merged exons of isoforms of each gene to calculate TPM (transcripts per kilobase of gene length per million total reads) for all protein-coding genes in each library. The GRCz11 repeat annotation was obtained from UCSC (Navarro Gonzalez et al 2021).…”

Chromatin accessibility associated with aquaculture relevant traits in tilapia

“…Given the large number of accessible peaks and overlapping genes (127,602 peaks and 20,248 genes), we devised an approach to reduce and identify the peaks that could regulate their gene targets expression. For gene expression, we use an approach applied previously 85 to calculate transcript per million (TPM) values by first normalizing the transcript count by the gene length, as calculated using GTFtools 86 , followed by the library size, as calculated using QualiMap (v 2.2.1) 83 , and then carrying out a log2 (x +1) transformation of 1) each genes TPM in each replicate; and 2) the mean TPM for each gene across biological replicates. Each genes mean TPM across the three replicates is used to assess correlations with ATAC signal whereas replicate specific TPM are used to study any differences between replicates.…”