Need new version : tx2gene.gencode.v47.csv
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Gaurav • 0
@14b5011f
Last seen 3 months 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 • 798 views
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Guido Hooiveld ★ 4.1k
@guido-hooiveld-2020
Last seen 5 months 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.

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I used Tximport recently. For that I had to use "tx2gene.gencode.v27.csv" which is very old. I made the new "tx2gene.gencode.v47.csv" and used it so that all the gene transcripts could be picked. I am unable to attach "tx2gene.gencode.v47.csv" here since it is 14 MB in size. Why don't you provide "tx2gene.gencode.v47.csv" in the tximportData folder itself so that normal users don't have to make it themselves? Every body is using Gencode.v47 now. You can simply upload it so that new users can download the latest v47 version while downloading tximport and tximportData via BioConductor using RStudio.

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