Homo_sapiens.GRCh38.91.chr.gtf.gz or Homo_sapiens.GRCh38.91.gtf.gz for differential expression of RNA-seq data?

Question

[amina.mcdiarmid]

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.

Answer 1

[Devon Ryan]

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.

[amina.mcdiarmid]

Thank you very much!

[hjsunbio]

Thank you very much, Your answer solved my question.