Question: hisat2 analysis and cuffdiff
0
gravatar for qudrat
4 months ago by
qudrat50
NATIONAL INSTITUTE OF IMMUNOLOGY, INDIA
qudrat50 wrote:

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?

ADD COMMENTlink modified 4 months ago • written 4 months ago by qudrat50

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

ADD REPLYlink written 4 months ago by WouterDeCoster30k

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.

ADD REPLYlink written 4 months ago by qudrat50
1

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.

ADD REPLYlink written 4 months ago by Devon Ryan81k

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.

ADD REPLYlink written 4 months ago by genomax52k
2
gravatar for Devon Ryan
4 months ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

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

ADD COMMENTlink written 4 months ago by Devon Ryan81k

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

ADD REPLYlink written 4 months ago by qudrat50

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

ADD REPLYlink written 4 months ago by Devon Ryan81k
0
gravatar for grant.hovhannisyan
4 months ago by
grant.hovhannisyan900 wrote:

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.

ADD COMMENTlink written 4 months ago by grant.hovhannisyan900
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