Import quant.sf files
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16 months ago
Andrea ▴ 10

Hi,

I have a problem in importing quant.sf files. I've already read a lot of posts, but I can't solve the issue. I have ~600 quant.sf files obtained from Dragen RNA analysis and they are all in the same folder. I would like to import them in R to make DE analysis and I also would like to obtain a counts and a TPM matrices. The output of Dragen has already the transcript ID, the length, the count and the TPM in each file.

Thank you!

tximport RNAseq tximeta • 924 views
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...and what is the problem? Instructions for salmon (that is the tool that produces these quant.sf files) to tximport is here: https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Salmon

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