inserting Normalized count data

Hello, Is there anyone here help me how input a dataset of normalized count data to Deseq2. Just I have normalized count I don`t know is (FPKM or TPM ) and what packages was used for alignment . is possible to find to know is fpkm or tmp?

best

deseq2

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updated 1.6 years ago by ATpoint

• written 1.6 years ago by Saeed •

2 answers

If you don't have raw counts data, it's probablly better to use an alternative pipeline like edgeR.

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written 1.6 years ago by yura.grabovska •

Neither DESeq2 nor edgeR can be used. If you only have these data then log2 and use limma-trend. Search the web. DE from FPKM has been asked so many times before. But seriously, get the raw data. It's neither reproducible nor publishable without.

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written 1.6 years ago by ATpoint

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