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How to import RSEM results to DESeq2 for differential analysis

The results of RSEM are expected counts of transcripts and genes and they are not integer. DESeq2, however, need a matrix of integer as input. The manual of RSEM said the results of RSEM can be used by DESeq. So my question is how to import non-integer RSEM counts to DESeq2 for downstream differential analysis? Thank you!

rsem deseq2
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updated by hosseini • hosseini • written by 402374688 • 402374688

Michael,

Thanks for your response. Could you please tell me why transcript-level counting is non-integer?

Thanks, Hadi

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written by hosseini • hosseini

Please do not ask unrelated questions in old threads, and please use the ADD COMMENT button, not the answer field. It is not integer because it is abundance estimates, not counts. tximport will then produce gene level counts.

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written by ATpoint ATpoint

1 answer

You can use tximport to import RSEM quants and then DESeqDataSetFromTximport() in DESeq2. The development version of tximport allows importing transcript-level abundances as well (previously just gene-level).

Edit 4.3.2020 by ATpoint since this thread gets a lot of views:

The manual contains example code on how to use RSEM output with tximport, which can then be processed with DESeqDataSetFromTximport()

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updated by ATpoint ATpoint • written by Michael Love Michael Love

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