Questions tagged [gencode]

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Why are my genes filtered for Gene Ontology term enrichment?

When I enter a list of gene names into common gene ontology (GO) term enricher (e.g. MsigDB or ToppGene) only a small fraction of genes is actually used for the enrichment: I am struggling to ...
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3 votes
1 answer

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

Starting with a chromosome # and position, I am trying to get chromStart and chromEnd values for a .bed file, but I am not sure how to calculate chromEnd when I have a variant that is an insertion or ...
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11 votes
2 answers

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

I have read counts data and I want to convert them into RPKM values. For this conversion I need the gene length. Does the gene length need to be calculated based on the sum of coding exonic lengths? ...
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45 votes
5 answers

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

What are the actual differences between different annotation databases? My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation)...
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