Presently, library(tximportData) contains "tx2gene.gencode.v27.csv". Can we get the latest "tx2gene.gencode.v47.csv"? Is it at all required or available?
Presently, library(tximportData) contains "tx2gene.gencode.v27.csv". Can we get the latest "tx2gene.gencode.v47.csv"? Is it at all required or available?
Assuming that you would like to import the results from salmon
, it is highly recommended to now use tximeta
. By doing so, all required files will be automatically downloaded and parsed.
See the workflow at https://bioconductor.org/packages/release/bioc/html/tximeta.html.
Note that you will first need to create a sample table (called coldata
in the workflow), that at least contains a column (should be labelled files
) that points to the location of the salmon
files, and a column (should be labelled names
) that contains the name of each sample. Obviously you could also add other data (columns) that contain information on the experimental group, subjectid, batch, etc a sample belongs to; thus info that would be needed later in the workflow.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.