Questions tagged [gtf]
Gene Transfer Format, a derivative of GFF, a tab-delimited plain-text format for describing gene annotations.
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I need to index a GTF (gene transfer format) annotation file
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 this error:
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Differences between Gencode GTF and Ensembl GTF files
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 biotypes/normalization lists etc, http://...
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Fastest way to convert GTF or GFF file to a BED file?
Given a GTF/GFF3 annotation file, what is the fastest way to convert it into a BED file?
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How can I convert a BED file to GTF/GFF with gene_ids?
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 this:
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building custom gtf file with entrez ID for any organism
How do I generate a custom gtf file format for a organism of my interest similar to human gtf file, in the custom gtf file I want to add entrez id to the new custom gtf.
My organism is ...
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Exon number between GTF file and ENSEMBL site does not match
Based on the ENSEMBL GTF file, I counted the number of exons per gene as follows:
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Stringtie/DEprep.py gene/transcript IDs are wrongly formatted
Hi my RNAseq workflow is ending up with wrongly formatted gene IDs (and separately transcript _IDs) after a Hisat2 ->samtools sort -> stringtie -> DEprep.py workflow.
DEprep.py outputs a ...
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Gencode PolyA feature annotation GTF gene_id not the same as Comprehensive gene annotation GTF
I have downloaded the Gencode PolyA feature annotation GTF here. The first 10 lines are like this:
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How to remove redundancy from a gtf file?
I have an annotation file. I would like to remove redundancy, as shown in the example (in the real file, I have a lot of these redundant cases).
I would like to consider only one of the following ...
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gtf2bed only retains gene information
I want to convert an hg38 GTF file to bed format using gtf2bed:
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On the same strand, for the same gene, can exons be overlapping?
I want to get a set of exon regions for each protein coding gene.
I extracted a set of relevant information (chromosome, start, end, gene ID, gene name, gene type, exon number and exon ID) from a GTF ...
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Extract only exon regions from GFF/GTF file with input bed regions
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 command or tool that ...
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GTF file format causing GeneMark-ES error
I am predicting genes using GeneMark-ES, I managed to generate a gtf file, but when I tried to extract the nt/protein sequence ...
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How to check if a fasta file and a GTF file fit and form a valid pair?
I'd like to know if there is a simple way to check the concordance between a GTF file and a fasta file (that I use as mapping reference) ?
It may be a dumb question, but I suspect discrepancies ...
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GTF parser for Python
I found this GTF parser for Python. However, it does not work with Scallop's GTF file:
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A .gtf file for HG38 for HISAT2 indexing
I am trying to build a HISAT2 index using Pertea et al. procedure (https://www.ncbi.nlm.nih.gov/pubmed/27560171) using their extract_splice_sites.py and ...
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How to convert gff to gtf?
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 sequences from ...
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A GTF annotation for GRCH375d version
I have been given a bunch of .bam files, that come from the alignment on GRCh37d5 of human genome by Star tool. I want to extract raw read counts from these bam files by FEATURECOUNTS tool so I need a ...
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Assembly by stringtie
I run this cmd
./stringtie G1_sorted.bam -B -o G1.gtf -G Triticum_aestivum.IWGSC.42.gtf -p 4 -C G1.refs.gtf -A G1.abund.tab
Error is:
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GTF from consensus sequence
I am new to using bioinformatic tools and I was hoping this community could help clear something up for me. I need to generate a gtf file. My data are a set of complete HA genes for influenza B ...
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Identify non-coding regions from a genome annotation
I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome:
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Making a bed file for RSeQC
I making a bed file for RSeQC, so it can do things like compute the number of reads from exons, introns, 5"UTRs, etc.
I want to use a bed file that corresponds to my GTF file, so I use gtf2bed to ...
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scRNA-seq, 10x cellranger pipelines
I'm starting to do sc-rnaseq using 10x cellranger pipelines, and i add TdTomato sequence to mouse reference genome and add an entry in the gtf. My code is But when I makref, it remindered that:
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Derive a GTF containing protein coding genes from a GTF file with Exons and CDS
Why I need a compatible file
I’m trying to run
velocyto with the R package to analyse RNA velocity (cell trajectories) with single cell RNASeq data. I have performed single cell analysis from 10x ...
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Parsing gtf file for transcript ID and transcript name
I used this previously to get ensembl ID and its gene name from the gencode gtf annotation file
This was the script I used
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Fast filtering of intervals not falling within a certain distance from known genes
I would like to filter a bed file with intervals, ie. in the format of:
chr1 13800 14301
chr1 15500 16001
chr1 19400 19901
chr1 22800 23301
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get gene lines from gtf file
I would like to retrieve gene lines from a GTF file for which I only have exons & transcripts lines (output from Cufflinks) and alternative splicing possible. I need gene lines for compatibility ...
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How to get rid of the temp files while using "featureCounts" for extracting readcounts from bam files?
I used this command for extracting read counts for almost 60 samples using featureCounts.
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Run gffread in multi-thread mode
Is there any possibility to run gffread in multi-thread mode? The answer seems to be 'no' from the manual (or gffread -h), as no multi-thread option is mentioned.
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seqret: Warning: bad /protein_id value
I am using the seqret tool from the Emboss suite to transform produce an EMBL annotation file from a GTF annotation file and the corresponding FASTA sequence:
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Counting reads for each biotype
I have bam files. I want to find the total read counts associated with all the biotypes, eg snRNA,rRNA,tRNA mRNA,scRNA,snoRNA etc. I can use ht-seq count to get read counts for the genes, but is ...
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5'UTR and 3'UTR annotation in yeast
I am working on a project in which I need to compute several parameters (such GC content and length) of 5'UTR and 3'UTR sequences of Saccharomyces cerevisiae yeast genes.
The problem is finding a ...
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How to provide a GFF/GTF file to Chromonomer
I am trying to use Chromonomer. It should be possible (according to the software page and a paper) to add a GFF/GTF file to the analysis.
Alas, neither the built-in help nor some light source code ...
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How can I calculate gene_length for RPKM calculation from counts data?
I have read counts data and I want to convert them into RPKM values. For this conversion I need the gene length.
Does the gene length need to be calculated based on the sum of coding exonic lengths? ...
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hg38 GTF file with RefSeq annotations
I'm not sure what I'm missing, but I'm struggling to find an official hg38 GTF file with RefSeq annotations. I'd like to provide ...
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Same transcript coordinates in gtf file, different transcript ID
I have a gtf file from Ensembl, and I noticed that several "transcript" annotations have the exact same coordinates. See for instance the third and fourth transcripts ("Y74C9A.2b.1" and "Y74C9A.2b.4") ...
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How to convert GFF3 to GTF2
I would like to convert a file in gff3 format to a gtf2.2 format.
The reason why I would like to do this is: I have a set of ...
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How to represent trans-spliced genes in GTF?
For example, see this gene (nad1) in ENA:
http://www.ebi.ac.uk/ena/data/view/ABI60879
If you look at the XML for that gene you see the following:
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What kind of "gff" format does bioawk parse?
I was wondering if I could use the gff parsing capability of bioawk to facilitate the parsing of gtf files, and I looked at the following help message:
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Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?
I got a customized GRCh38.79 .gtf file (modified to have no MT genes) and I need to create a reference genome out of it (for 10xGenomics CellRanger pipeline). I suspect that the .79 part is the ...
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