RSEM for DESeq2 without abundance matrix
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le2336 ▴ 20
@le2336-10789
Last seen 2.1 years ago

I am working with RSEM outputs of RNA-seq data that I downloaded from a repository as .tsv files. I would like to apply VST to this data by first using tximport to import the RSEM outputs. However, the RSEM outputs from this repository only include the lengths and estimated counts, and are missing the abundance information. Would it still be possible to use these data with tximport and DESeq2?

Thanks very much.

tximport deseq2 rsem • 484 views
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@mikelove
Last seen 20 hours ago
United States

No, tximport will give an error without the abundances.

If you have the gene-level counts and lengths, you can import the data manually and use DESeqDataSetFromMatrix with the counts matrix (rounded to integers). Then you can assign the lengths matrix as:

assays(dds)[["avgTxLength"]] <- ...


And this will then behave as if you had imported with tximport (one caveat is that you should make sure there are no genes with length of 0 -- tximport ensures this does not happen but it can occur with RSEM lengths).

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Thank you, this works great!