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* Internet Search Results    *** Search Filter: "GTF"    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. 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 ... 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 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). rna seq - ribo interval list for picard ensembl mm9 gtf ... Edit: To make a file compatible with picard's "interval list", one can do the following with the GTF file: grep rRNA foo.gtf | awk 'BEGIN{OFS="\t"}{print $1, $4-1, $5}' > foo.bed According to the picard documentation a BED file can be used as input and the above awk code extracts the appropriate columns and switches to 0-based coordinates used ... Newest 'gtf' Questions - Bioinformatics Stack Exchange 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. 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: 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 canis_familaris. I have to use is this source. How do I start, is there any tools there to build custom gtf file from the GENE_INFO file? Ensembl vs Gencode - Bioinformatics Stack Exchange 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 ...       FIRE101 Jobs:    FIREMEN, EMS, Emergency, Rescue   POLICE101 Jobs:    Cops,Officers,Security   Mainframe IT Jobs:    z/OS, z/VM, DB2, COBOL,QA,INTERNs   Software Jobs:    Web, Linux, C++, Java, INTERNs   Finance Jobs:    Accounting, INTERNS, Brokers, Invest   Legal, Lawyer Jobs:    Paralegals, INTERNs,Law Firms   Medical, Nurse Jobs:    Doctors, INTERNs, Nurses, ER   Genetic, Science Jobs    Genetics, Research, INTERNs, Labwork * Latest zVM Mainframe News        *** News Filter: "GTF"