Which reference genome, DNA or cDNA and why?
0
0
Entering edit mode
5 months ago
وفاء • 0

Dear Community,

The goal of my study is analyze Human RNA-seq and to take the gene count for RNA-seq and then apply the DESq2. I must use the most recent genome reference, but I am unsure of which FASTA file to use from Ensembl.

DNA or cDNA and why?

Best,

or DNA cDNA • 490 views
ADD COMMENT
1
Entering edit mode

What tool are you using for your reads?

If you're using kallisto, salmon, or rsem, you use cDNA (coding DNA [aka transcriptome]) reference from ENSEMBL. It can be downloaded here: https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz

ADD REPLY

Login before adding your answer.

Traffic: 1571 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6