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Old 03-05-2019, 06:50 AM   #1
NDUFB11
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Default 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
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Old 03-05-2019, 07:37 AM   #2
GenoMax
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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).
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Old 03-05-2019, 07:44 AM   #3
NDUFB11
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Thank you genoMax for your answer,

can you tell me how this reads are normalized?

thanks
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Old 03-05-2019, 07:49 AM   #4
GenoMax
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You will get raw counts from featureCounts. You will need to use DESeq2/edgeR etc to actually do normalization and analysis.
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Old 03-05-2019, 07:59 AM   #5
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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

Last edited by NDUFB11; 03-05-2019 at 08:03 AM.
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Old 03-05-2019, 08:54 AM   #6
GenoMax
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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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