Question

R program for normalization of RNA seq counts data with Edge R or Deseq

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6.2 years ago

maryak ▴ 20

Can anybody guide me about normalization of RNA seq( Htseq-counts data ) using edgeR or Deseq2,i need help about R program for normalization of RNA seq using EdgeR.

RNA-Seq R sequencing • 5.6k views

ADD COMMENT • link 6.2 years ago by maryak ▴ 20

score 2 · Answer 1 · 2018-09-26

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6.2 years ago

GenoMax 147k

Normalization of the data is managed by the packages mentioned. You need to feed them raw count data.

ADD COMMENT • link 6.2 years ago by GenoMax 147k

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problem is i don't know the exact way of using these packages and feeding data to them

ADD REPLY • link 6.2 years ago by maryak ▴ 20

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Workflow for DESeq2 is described in detail here. For edgeR you can find similar information here.

ADD REPLY • link 6.2 years ago by GenoMax 147k

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In addition, focus on the section in the DESeq2 manual, htseq-count input.

ADD REPLY • link 6.2 years ago by ATpoint 85k

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i have ht-seq-count input in the form of excel file(CSV) but in these link i am not able to find how to normalize such kind of files..

ADD REPLY • link 6.2 years ago by maryak ▴ 20