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Questions tagged [gencode]

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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, http://...
Freek's user avatar
  • 573
1 vote
0 answers

Comparing common genes and transcripts between Gencode and Refseq

This is a very naive question - I am trying to compare and get the common lncRNA genes and transcripts between Gencode and Refseq from their gff files. Since their gene_id, gene_names are different, ...
beepboopbeep's user avatar
1 vote
1 answer

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

I have downloaded the Gencode PolyA feature annotation GTF here. The first 10 lines are like this: ...
justinian482's user avatar
3 votes
0 answers

Genome-guided transcriptome reconstruction: should I filter my reference annotation by transcript_support_level or other tags?

Is there really any advantage to filtering the GTF annotation for transcriptome reconstruction (or, for example, for pseudo-alignment quantification)? Are there any downsides (i.e. reasons why I ...
bepoli's user avatar
  • 175
0 votes
1 answer

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 ...
Tapper's user avatar
  • 67
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 ...
Sarah's user avatar
  • 516
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? ...
stack_learner's user avatar
48 votes
6 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)...
Plasma's user avatar
  • 583