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- Fastest way to convert GTF or GFF file to a BED file?
Given a GTF GFF3 annotation file, what is the fastest way to convert it into a BED file?
- Differences between Gencode GTF and Ensembl GTF files
I recently switched from RSEM to Salmon for RNAseq data processing I started in the Ensembl world and wrote a lot of code around their GTF file (for filtering biotypes normalization lists etc, htt
- 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 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
- 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
- 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
I mean, GTF is basically GFF2 Would it be OK to just remove the attributes? What information do you need to keep? Basically, what will you use the GTF for? Do you need the gene_id and transcript_id fields and, if so, where would that information come from? It might be helpful if you came into our chat room If you do, ping me (@terdon) to let
- read mapping - Can I run STAR without an annotation file . . .
It suggests I should use a GTF file But this is a draft genome of an individual for which no GTF is available I could try to adapt a GTF from a close relative but for the scaffolding, it seems superfluous Is there a way I can map with STAR without the GTF? These commands were run on a GNU Linux machine
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