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Internet Search Results
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.
Differences between Gencode GTF and Ensembl GTF files
(The biologists I work with like HUGO symbols so I make dictionary based on the GTF file). My last question is, for Gencode, there is a gencode.v46.annotation.gtf.gz and a gencode.v46.primary_assembly.annotation.gtf.gz at first glance they look the same but they do have a different number of lines (3467161 vs 3467739, not a big difference..)
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...
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).
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 ...
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...
How drastic would the result be if I use fasta or reference assembly ...
For fasta/GTF files from early in the GRCh38 release, you can tell whether you're using UCSC or Gencode by the presence/absence of _random contigs, which will only exist for UCSC. These were mostly later split into the actual contigs, so recent download from UCSC should more closely match what you find at Gencode/Ensembl.
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.
Can a gff file be converted to a fasta file? - Bioinformatics Stack ...
I extracted the sequence contained in the gff file into a separate file and added a header according to the fasta file format specifications.
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