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How to convert gff to gtf? - Bioinformatics Stack Exchange
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 the P Falicparum 3D7.
How to convert GFF3 to GTF2 - Bioinformatics Stack Exchange
GFF3_to_GTF utility in the FML package (./gff3_to_gtf_converter.pl input.gff3 output.gtf): the output just contains a header (##gff-version 2.5) and the log is empty; The gff3 file was created as output of GMAP, and contains the transcripts as found by alignment to the reference (specifying option -f gff3_match_cdna).
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: A USER ERRO...
Fastest way to convert GTF or GFF file to a BED file?
Besides the easy way to make gxf2bed run and the GFF-GTF channel that allows centralize both in a single converter, this tool showed a significant difference in computation time against the other tools in each one of the two formats. Even using a combination of different number of threads, times were practically the same 3.5s +/- 0.4s and the ...
Subset GTF file for specific genes - Bioinformatics Stack Exchange
$\begingroup$ You could add import pandas as pd and then try df.to_csv(out_filename, sep='\t') to write out a tab-delimited file from various data frame columns.
Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference ...
Further, for the GTF file differences: The only exception is that the genes which are common to the human chromosome X and Y PAR regions can be found twice in the GENCODE GTF, while they are shown only for chromosome X in the Ensembl file. Gencode(Ensembl) vs RefSeq. Gencode is in almost all cases more comprehensive. For example, this is NCBI ...
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: chr27 17266469 172...
GTF parser for Python - Bioinformatics Stack Exchange
I found this GTF parser for Python. However, it does not work with Scallop's GTF file: chr01_pilon_pilon scallop transcript 168145 169166 1000 .
Derive a GTF containing protein coding genes from a GTF file with Exons ...
In your case, I would definitely suggest following @Emily_Ensembl's advice and using the Arabidopsis GTF from Ensembl. But for future reference, if an Ensembl GTF wasn't available, you could build something like this using the gtf class from cgat. The cgat module and dependancies can be installed by following the instructions here. Specifically ...
Extract only exon regions from GFF/GTF file with input bed regions
$ gtf2bed < annotations.gtf | grep -wF exon > exons.bed $ sort-bed myRegions.unsorted.bed > myRegions.bed $ bedops --element-of 100% exons.bed myRegions.bed > answer.bed Or as a one-liner, which is even faster:
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