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24 votes
Accepted

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

To add to rightskewed answer: While it is true that: Gencode is an additive set of annotation (the manual one done by Havana and an automated one done by Ensembl), the annotation (GTF) files are quite ...
Mitra's user avatar
  • 504
12 votes

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

Ensembl vs Gencode https://www.gencodegenes.org/faq.html The GENCODE annotation is made by merging the Havana manual gene annotation and the Ensembl automated gene annotation. [...] In practical ...
Saket Choudhary's user avatar
7 votes

How can I calculate gene_length for RPKM calculation from counts data?

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 ...
Devon Ryan's user avatar
  • 19.7k
6 votes

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

To add practical advice to what others have said: In a practical sense, I think the biggest difference between RefSeq and Ensembl/GENCODE is in the sensitivity/specificity trade off. Ensembl aims ...
Ian Sudbery's user avatar
  • 3,321
3 votes

Differences between Gencode GTF and Ensembl GTF files

Let me answer around your questions a bit freely: Gene Versions: I always gsub them away when using GENCODE since the actual version control happens by using a fixed and reproducible GENCODE release. ...
ATpoint's user avatar
  • 1,430
2 votes
Accepted

Gencode PolyA feature annotation GTF gene_id not the same as Comprehensive gene annotation GTF

According to the GENCODE ftp README file, the value of the 'gene_id', 'transcript_id', 'gene_name' and 'transcript name' fields corresponds to a random identifier. The polyA features are not directly ...
JoseM's user avatar
  • 36
1 vote
Accepted

Why are my genes filtered for Gene Ontology term enrichment?

What is "click here for details" saying? That link should contain an explanation of what happened. GSEA usually requires entrez_id to run. If your list contains <...
fra's user avatar
  • 567
1 vote

Dealing with indels when converting a position to chromStart and chromEnd for a bed file

You can convert to VCF and use BEDOPS vcf2bed --insertions, vcf2bed --deletions and ...
Alex Reynolds's user avatar
1 vote

How can I calculate gene_length for RPKM calculation from counts data?

I assume you are mapping against the genome rather the transcriptome, since for the later the length would be trivial. Assuming the first, I think not only the coding sections should be included but ...
Sebastian Müller's user avatar
1 vote

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

The UCSC Genome Browser Genes FAQ discusses this question in detail: https://genome.ucsc.edu/FAQ/FAQgenes.html#ens Officially, the Ensembl and GENCODE gene models are the same. On the latest ...
Max's user avatar
  • 111
1 vote

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

While annotations between RefSeq and Gencode are not so different is the coding regions (genes), Gencode is much more rich in the intergenic regions. This could be very advantagous for epigenetic ...
Zz...zZ's user avatar
  • 11

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