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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 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)
GTF To Use With Broad Institute Fasta In STAR 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
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:
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