Closed:How to obtain list of reference genes for RNA-seq analysis
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11 months ago
nkabo ▴ 50

Hi,

I am working on RNA-seq analysis and I am a very beginner. For indexing and quantification, I had used salmon https://combine-lab.github.io/salmon/getting_started/. Now, I try using DESeq2 in R to finalize the analysis. However, for the latest part of the analysis, I need a list of reference genes. I am currently using a colleague's workflow and the list of reference genes is entitled in the script as "mart_export.txt". I tried to download such a list from biomaRt and Ensembl, but I could not find the whole human reference gene list (ensembl only gives a few genes), I could only reach a FASTA file. I am looking for something with Ensembl gene ids and gene names.

How could I reach such .txt file?

Thanks a lot!

RNA-Seq R biomaRt salmon DESeq2 • 123 views
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