Fastest way to convert GTF or GFF file to a BED file?
Feb 6, 2024 · Given a GTF/GFF3 annotation file, what is the fastest way to convert it into a BED file?
How to convert gff to gtf? - Bioinformatics Stack Exchange
Dec 29, 2019 · My annotation file is in .gff format. I would like to convert it to .gtf format or to know if there is a way to directly download the annotation file in .gtf format? I am working on …
Differences between Gencode GTF and Ensembl GTF files
May 30, 2024 · I recently switched from RSEM to Salmon for RNAseq data processing. I started in the Ensembl world and wrote a lot of code around their GTF file (for filtering …
read mapping - Can I run STAR without an annotation file ...
May 26, 2018 · It suggests I should use a GTF file. But this is a draft genome of an individual for which no GTF is available. I could try to adapt a GTF from a close relative but for the …
How can I convert a BED file to GTF/GFF with gene_ids?
Dec 2, 2023 · Given a .bed (BED12), how can I convert it to GTF/GFF formats with gene_id attributes? What is the fastest way or available tools to do it? For example, given an input like …
I need to index a GTF (gene transfer format) annotation file
Sep 18, 2024 · This question was also asked on Biostars I created a GTF file for HLA alleles to be used as a resource for GATK Funcotator. Running Funcotator without indexing the GTF gives …
gene - How can I calculate gene_length for RPKM calculation from …
Sep 26, 2017 · In Github I have seen RPKM calculation from Counts data with the Gene_length from Gencode GTF file. Do you think this is the right way of calculation? And why RPKM is - …
Extract only exon regions from GFF/GTF file with input bed regions
Mar 3, 2022 · I have a bed file that contains a list of regions and I would like to extract only the exon regions from a GTF/GFF file that are contained in the given regions. Is there a simple …
How to convert GFF3 to GTF2 - Bioinformatics Stack Exchange
Jul 15, 2017 · I mean, GTF is basically GFF2. Would it be OK to just remove the attributes? What information do you need to keep? Basically, what will you use the GTF for? Do you need the …
GTF To Use With Broad Institute Fasta In STAR
Aug 23, 2023 · To make a STAR reference genome used for alignment you need a genome fasta (the resources fasta provided by the Broad Institute in my case) and a GTF fasta. I tried to use …