hisat2 analysis and cuffdiff

Question

[qudrat]

Hello all,
I have two BAM files obtained by HISAT2 and I want to see differential expression of some genes. Can I use Cuffdiff to see the differential expression?

[WouterDeCoster]

You haven't learned a lot from previous threads, have you?

[qudrat]

Actually the aim of experiment is to find differentially expressed genes between a drug treated and a non-treated cell line sample. Two BAM file were produced; one for each sample using HISAT2, now I want to see the differentially expressed genes.

[Devon Ryan]

That study wasn't designed in a way that an answer could be obtained. A sensible design would have been to use multiple passages or at least multiple plates of the same cell line. Otherwise you don't know if differences are just due to things like plate confluence or treatment.

[GenoMax]

qudrat : Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. Submit Answer should only be used for new answers for original question.

Answer 1

[Devon Ryan]

With two BAM files you can't accurately assess differential expression with any tool.

[qudrat]

I can include more BAM file in my study, then would it be possible to use Cuffdiff?

[Devon Ryan]

I don't know of anyone that has a high opinion of cuffdiff, but yes you could then use it.

Answer 2

[grant.hovhannisyan]

You can, but it will be meaningless. Tell us more about experimental design of your study, we can't help you if you don't provide specific details.