single-cell exome sequencing pipeline

Question

[zizigolu]

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?

[WouterDeCoster]

What do you mean with founder organism? Single cell exome sequencing will indeed require an adapted pipeline...

[zizigolu]

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?

[WouterDeCoster]

Adapted, meaning different specifically for this technology and aim. So you have performed exome sequencing for many tissues of the same mouse?

[zizigolu]

actually I don't know exactly I will be givven the fastq files but my mentor told as below

[WouterDeCoster]

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!

[zizigolu]

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?

[WouterDeCoster]

This is the most commonly accepted "standard" workflow for WES: GATK best practices

[zizigolu]

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

[WouterDeCoster]

You need more information about how the sequencing data will be prepared.

[zizigolu]

thank you @WouterDeCoster

[zizigolu]

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?

[WouterDeCoster]

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.

[zizigolu]

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

[WouterDeCoster]

You can find something about comparing soap to bwa here: A: Comparison Of Soap And Bwa