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!
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Have you seen the vignette on importing
salmonresults into DESeq2 for analysis.Thank you for your reply, I checked it, but I am not familiar with what they mean by "samples.txt" file. I have only two subjects and I have paired end reads (subject1.R1.fastq, subject1.R2.fastq, subject2.R1.fastq, subject2.R2.fastq), in total; I have four .fastq files.
Should I generate such samples.txt file by myself?
Also, I could not quite understand what should it be located under samples$run in the vignette.
Ensembl is currently under maintenance. You need it to add the gene names to the results file, since the salmon output only had the ensembl ids?
Thank you for your reply, I need the gene names corresponding to the gene ids.
Can you please give an example? I am not familiar with the term "reference gene" in this context despite having using salmon and DESeq2. Do you mean the tx2gene map to match each transcript to its corresponding gene?
Thank you for your reply, I have the tx2gene output as tx2gene.Homo_sapiens.GRCh38.100.csv. I need such file to have the gene names.
Unclear what you mean.