How to seperate the groupA and B in Linux

[Bo Zhu]

Hi,

  Due to the large Bam file, I am using linux version of SAMMate. I am wondering how it recognize the different groups as in windows version. Because from command line it only mentioned to use the comma.

Best

Bo

[Dongxiao Zhu]

Hi, SAMMate uses edgeR Bioconductor package to detect differentially expressed genes. After you get read counts, please load edgeR and follow the commands below. It represents two groups with two replicates in each group.

 

Best,

 

Dongxiao

 

> x <- read.delim("fileofcounts.txt",row.names="Symbol")

> group <- factor(c(1,1,2,2))

> y <- DGEList(counts=x,group=group)

> y <- calcNormFactors(y)

> y <- estimateCommonDisp(y)

> y <- estimateTagwiseDisp(y)

> et <- exactTest(y)

> topTags(et)

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[Tin Nguyen Chi]

Hi Bo,

The current linux version of SAMMate does not have the module to group
the input as the Windows version. Sorry for the inconvenience, we hope
to upgrade it soon.

Thanks

[Bo Zhu]

Thanks for you guys reply. It will be really cool to add this function like Trinity. Meanwhile, I am wondering if next version can add a memory usage on Windows GUI version as it always occupy all my memories...

Best

Bo

在 2013年8月19日星期一UTC+2下午9时07分14秒，Tin Nguyen写道：