Entering edit mode
7.4 years ago
zizigolu
★
4.3k
hi,
I found some threads about mutation calling from exome-seq pipelines but if the pipeline is different when we have many independent samples from founder organism?
What do you mean with founder organism? Single cell exome sequencing will indeed require an adapted pipeline...
thank you, Founder organism here is the mice with oncogene which causes to cancer and we have many independent sample from this mice.
sorry what is an adapted pipeline?
Adapted, meaning different specifically for this technology and aim. So you have performed exome sequencing for many tissues of the same mouse?
actually I don't know exactly I will be givven the fastq files but my mentor told as below
This doesn't sound like single cell exome sequencing to me. Just a comparison before and after disease arises, am I right?
Okay, what would be your idea to solve this? I've no experience with sequencing mice (but can't be much different from human exomes). I'll provide feedback if you do some suggestions!
thank you,
thank you
actually "many independent leukemias from one ”founder” mouse" made me confuse but I can't ask my mentor if this means single-cell or not.
however I searched and I found for example a pipleline for exome-seq here
What Is The Best Pipeline For Human Whole Exome Sequencing?
This is the most commonly accepted "standard" workflow for WES: GATK best practices
sorry
I have to present a talk about my idea with pipeline, I remember something when my mentor told this is not simply mixing data and is a single-cell exome-seq
You need more information about how the sequencing data will be prepared.
thank you @WouterDeCoster
sorry,
although irrelevant with this threat, may you please give me some consult
my mentor asked me to write a proposal about What pipeline I would apply to identify any potential mutations from exom-seq data now is it enough to mention GATK best practice steps in word file or a proposal is something else?
I have no way to know how detailed your mentor wants that proposal. The GATK best practices are very well documented and contain lots of information, so I would suggest to read through those guidelines.
sorry,
here I found SOAP for exom-seq while in common pipelines there is nothing about SOAP
am I wrong?
http://www.cell.com/cms/attachment/2021776206/2041644626/figs3_lrg.jpg
You can find something about comparing soap to bwa here: A: Comparison Of Soap And Bwa