Using tximport to create the input for DESeq2
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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
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@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.