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
2.3 years 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 • 2.8k views
ADD COMMENTlink modified 2.3 years ago by Devon Ryan95k • written 2.3 years ago by amina.mcdiarmid0
1
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k 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 2.3 years ago by Devon Ryan95k

Thank you very much!

ADD REPLYlink written 2.3 years ago by amina.mcdiarmid0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 813 users visited in the last hour