I need to index a GTF (gene transfer format) annotation file
2024年9月18日 · 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 gff to gtf? - Bioinformatics Stack Exchange
2019年12月29日 · 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
2017年7月15日 · 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).
GTF To Use With Broad Institute Fasta In STAR
2023年8月23日 · 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 the Ensembl human genome fasta fro hg38 but that does not work. I have looked in the GATK resources package but there is no .gtf file there. I really don't know what to do in ...
Differences between Gencode GTF and Ensembl GTF files
2024年5月30日 · (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..)
Fastest way to convert GTF or GFF file to a BED file?
2024年2月7日 · 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
2021年9月6日 · $\begingroup$ 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.
How drastic would the result be if I use fasta or reference assembly ...
2019年6月13日 · 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.
How can I convert a BED file to GTF/GFF with gene_ids?
2023年12月2日 · 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...
Feature annotation: RefSeq vs Ensembl vs Gencode, what's the …
2017年5月16日 · 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 …