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-   -   RNAseq from patients (http://seqanswers.com/forums/showthread.php?t=88009)

NDUFB11 03-05-2019 06:50 AM

RNAseq from patients
 
Hello,
I have a question, If I have 10 Bam files (RNAseq) from 10 different patients and I want to see the different expression of few genes, what is the best tool to use after counting the reads?

Thank you

GenoMax 03-05-2019 07:37 AM

featureCounts part of Subread package. You can feed all your BAM files at the same time to get a matrix of counts (rows as genes and columns as your samples).

NDUFB11 03-05-2019 07:44 AM

Thank you genoMax for your answer,

can you tell me how this reads are normalized?

thanks

GenoMax 03-05-2019 07:49 AM

You will get raw counts from featureCounts. You will need to use DESeq2/edgeR etc to actually do normalization and analysis.

NDUFB11 03-05-2019 07:59 AM

but if I use Deseq2 it requires biological replicates, which I don't have it in my case.

How can I create the data frame and the condition with DESq2 in this case?

thank you

GenoMax 03-05-2019 08:54 AM

You can use DESeq2 without replicates. It is not recommended. Your analysis would not have any statistical significance.

Hopefully you have some other condition that you could test on?


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