Need new version : tx2gene.gencode.v47.csv
1
0
Entering edit mode
@14b5011f
Last seen 6 hours ago
India

Presently, library(tximportData) contains "tx2gene.gencode.v27.csv". Can we get the latest "tx2gene.gencode.v47.csv"? Is it at all required or available?

tximportData • 231 views
ADD COMMENT
0
Entering edit mode
Guido Hooiveld ★ 4.1k
@guido-hooiveld-2020
Last seen 11 days ago
Wageningen University, Wageningen, the …

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.

ADD COMMENT

Login before adding your answer.

Traffic: 627 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