matrix with Salmon gene-level quantifications in DESeq
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luca.s ▴ 10
@lucas-24386
Last seen 27 days ago
Italy

Hi all. I am in the need of analyzing RNAseq data that are available in the form of a matrix with Salmon quantifications summarized at gene level (non-integer values). Can they be used as an input for DESeq, and what would be the best way to do this? I am providing a sample of the table below (apologies for the formatting). Thank you for the help. Luca

Sample_A Sample_B Sample_C A1BG 131.084 124.366 172.048 A1CF 3 6 8.856 A2M 24.212 36.87 14.873 A2ML1 1212.969 40.953 53.881

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@james-w-macdonald-5106
Last seen 19 minutes ago
United States

Use the tximport package.

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Thanks James for the quick answer, but does the tximport package work also for importing a single matrix in which are contained all gene quantifications for all samples? Sorry for the naive question, but I understood from the vignette that it handles only the original Salmon output.

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I feel like this is definitely covered in the vignette. We show importing multiple samples to gene level.

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ATpoint ▴ 720
@atpoint-13662
Last seen 17 minutes ago
Germany

If you have quantifications on the transcript level and want to go to the gene level then use the methods described in tximport.

If you already have a matrix with gene level counts then load it into DESeq2 with DESeq2::DESeqDataSetFromMatrix, requiring that rows are genes and columns are samples.

Given that you seem to have the original salmon quantifications, I would recommend to not do any custom approach but simple aggregate the salmon transcript level abundence estimates (so the quant.sf files) to the gene level with tximport as described in this link:

https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Salmon

...and then port it over to DESeq2 with DESeq2::DESeqDataSetFromTximport. That can be done in very few lines of code and you can be sure the data (e.g. the length estimates) will end up at the required slots in the dds object to be correctly used downstream.

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Thanks all for for dissecting the point and sorry for the late feedback. Unfortunately, I only had the matrix of gene level counts, so I went through DESeqDataSetFromMatrix. Hope this does not impact the tresults too much.

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How would you have a gene-level matrix from salmon?

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tximport from a collaborator

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