Using tximport to create the input for DESeq2
1
0
Entering edit mode
ahmesalama • 0
@17074d71
Last seen 6 weeks ago

Hello,

I have the StringTie output files and need to run DGE using DESeq2. I ran the following code:

library(tximport) <- read_tsv("t_data.ctab"[1]) tx2gene <- tmp[, c("t_name", "gene_name")]

With that I was able to extract t_name and gene_name columns. But this was for only one sample.

However, when I execute txi <- tximport(files, type = "stringtie", tx2gene = tx2gene) I got an error. What does "files" mean in this last code? I suppose files refer to t_data.ctab files (one for each sample), is that right? Nevertheless, in the tx2gene there is only one sample processed. How I can merge the "t_data.ctab" files to get the data matrix needed for DESeq2? May you please provide the detailed script to do so?

Thank you.

RNASeqR • 112 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 19 minutes ago
United States

FYI: you should in the future tag posts with the package name, e.g. "tximport" to notify the maintainer.

Did you see the StringTie example in the vignette? tx2gene should be a table linking transcripts to genes, if this is sample-specific then you can't use tximport, you'll need to some kind of pipeline that produces output that is consistent across samples.

ADD COMMENT

Login before adding your answer.

Traffic: 404 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