Questions tagged [gtf]

Gene Transfer Format, a derivative of GFF, a tab-delimited plain-text format for describing gene annotations.

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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?
Alejandro Gonzales-Irribarren's user avatar
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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: ...
Alejandro Gonzales-Irribarren's user avatar
1 vote
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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 ...
kcm's user avatar
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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 ...
RichardBJ's user avatar
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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: ...
justinian482's user avatar
3 votes
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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 ...
Marco's user avatar
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gtf2bed only retains gene information

I want to convert an hg38 GTF file to bed format using gtf2bed: ...
justinian482's user avatar
4 votes
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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 ...
gc5's user avatar
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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 ...
SBDK8219's user avatar
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Subset GTF file for specific genes

I have a GTF file (in 'test.gtf' file): ...
justinian482's user avatar
2 votes
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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 ...
Abi's user avatar
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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 ...
elielink's user avatar
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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: ...
user977828's user avatar
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2 answers
445 views

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 ...
Dmitrii Trubetskoy's user avatar
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4 answers
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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 ...
Diango's user avatar
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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: ...
fatima's user avatar
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3 answers
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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 ...
Lindsey's user avatar
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6 votes
3 answers
785 views

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: ...
Zizogolu's user avatar
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4 votes
1 answer
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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 ...
Freek's user avatar
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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: ...
sophia's user avatar
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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 ...
Tom Kelly's user avatar
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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 ...
kcm's user avatar
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438 views

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 ...
gc5's user avatar
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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 ...
aechchiki's user avatar
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2 votes
1 answer
383 views

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. ...
beginner's user avatar
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6 votes
1 answer
360 views

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. ...
aechchiki's user avatar
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1 vote
1 answer
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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: ...
Biomagician's user avatar
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545 views

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 ...
user3138373's user avatar
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bed file to gtf conversion using awk

I have a bed file like this: ...
user3138373's user avatar
9 votes
2 answers
2k views

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 ...
plat's user avatar
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2 votes
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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 ...
Tássio's user avatar
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11 votes
2 answers
5k views

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? ...
stack_learner's user avatar
5 votes
1 answer
4k views

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 ...
Mark Ebbert's user avatar
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6 votes
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567 views

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") ...
bli's user avatar
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9 votes
3 answers
3k views

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 ...
aechchiki's user avatar
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4 votes
1 answer
106 views

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: ...
Dan's user avatar
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4 votes
1 answer
343 views

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: ...
bli's user avatar
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6 votes
1 answer
238 views

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 ...
Glrs's user avatar
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