Question: Homo_sapiens.GRCh38.91.chr.gtf.gz or Homo_sapiens.GRCh38.91.gtf.gz for differential expression of RNA-seq data?
0
gravatar for amina.mcdiarmid
16 months ago by
amina.mcdiarmid0 wrote:

I am carrying out RNA-seq analysis and need the annotation in GTF format from Ensembl to go with my reference sequence in fasta format.

Which of these is the correct one to use? ftp://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/

I can't work out whether I want the Homo_sapiens.GRCh38.91.chr.gtf.gz or Homo_sapiens.GRCh38.91.gtf.gz file.

annotation rna-seq ensembl genome • 1.7k views
ADD COMMENTlink modified 16 months ago by Devon Ryan90k • written 16 months ago by amina.mcdiarmid0
1
gravatar for Devon Ryan
16 months ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

You want the one without chr in the name. The one with chr is a subset of this, containing only chromosomes and not any unplaced contigs. Since you're presumably aligning against unplaced contigs already (if not, you should be), you might as well include them for consistency.

ADD COMMENTlink written 16 months ago by Devon Ryan90k

Thank you very much!

ADD REPLYlink written 16 months ago by amina.mcdiarmid0
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