I'm trying to run a differential expression analysis of 2 samples of the same species, but with different treatments using DESeq2. I'm using Ensembldb to create a tx2gene dataframe for tximport, however tximport does not select the columns I specify, and instead always selects the tx_biotype leading to the following output:
. 25_quant 28_quant nontranslating_CDS 10422.41 10022.74 protein_coding 22196722.59 24002269.26
I'm running tximport using the following params:
txi_tx <- tximport(files, type = "salmon", tx2gene = tx2gene, txIdCol = "tx_id", geneIdCol = "gene_id")
I've gotten around this by deleting all columns from my tx2gene DF apart from tx_id and gene_id. However, I think this might be causing problems in the DESeq2 analysis somehow, and I would like to rule out that possibility.
This is what my
names(tx2gene) looks like:
"tx_id" "tx_biotype" "tx_seq_start" "tx_seq_end" "tx_cds_seq_start" "tx_cds_seq_end" "gene_id" "tx_name"
What am I doing wrong?