RNAseq from patients

[NDUFB11]

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]

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]

Thank you genoMax for your answer,

can you tell me how this reads are normalized?

thanks

[GenoMax]

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

[NDUFB11]

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]

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?