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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
gene - How can I calculate gene_length for RPKM calculation from counts . . . Here you can find some example R code to compute the gene length given a GTF file (it computes GC content too, which you don't need) This uses one of a number of ways of computing gene length, in this case the length of the "union gene model" In this method, the non-duplicated exons for each gene are simply summed up ("non-duplicated" in that no genomic base is double counted) This is a