Question: hisat2 analysis and cuffdiff
0
gravatar for qudrat
5 weeks 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 5 weeks ago • written 5 weeks ago by qudrat50

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

ADD REPLYlink written 5 weeks ago by WouterDeCoster27k

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 5 weeks 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 5 weeks ago by Devon Ryan78k

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 5 weeks ago by genomax46k
2
gravatar for Devon Ryan
5 weeks ago by
Devon Ryan78k
Freiburg, Germany
Devon Ryan78k wrote:

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

ADD COMMENTlink written 5 weeks ago by Devon Ryan78k

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

ADD REPLYlink written 5 weeks 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 5 weeks ago by Devon Ryan78k
0
gravatar for grant.hovhannisyan
5 weeks ago by
grant.hovhannisyan730 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 5 weeks ago by grant.hovhannisyan730
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