Question: Are datasets for a unique cells, that downloded using sratoolkit?
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gravatar for ee.mohseni.alert
5 months ago by
ee.mohseni.alert0 wrote:

I use sratoolkit to download datasets, but I I do not know they are for unique cells or not? I want unique single sequencing for unique cells.

sequencing rna-seq • 138 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by ee.mohseni.alert0

Majority of the datasets in SRA are NOT going to be for single cell sequencing. You will need to specifically search with a term such as singlecell.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax84k

Thank for your guidance, I am beginning to analysis single cell sequencing and some issues are vague to me.

I want inference tumor phylogeny tree from SCS data, but in downloading data I have confused! how can I download and compare some different cell genomes in a tumor (for specific locus), ie. CRC?

I want SRXs samples that are for different cells in a specific locus.

Next question is that in SRP074289 samples, for example, Sample CO8 and CO5 are related to two different cells or they are related to different locuses for the same cell?

ADD REPLYlink written 5 months ago by ee.mohseni.alert0

What exactly is the question you want to answer? I understand you are looking for cancer single-cell data. So I assume whole genome data, right? Not RNA-seq or something like that. If so, what do you want to analyze? Mutations?

ADD REPLYlink written 5 months ago by ATpoint35k

Yes, it is. I want whole genome data. I want use SNV and CNV profile from different cells (tumor heterogeneity) to inference phylogeny tree.

Where can I download proper dataset?

ADD REPLYlink written 5 months ago by ee.mohseni.alert0

You could look for papers that use a package like sciclone ( https://github.com/genome/sciclone ). Possible search example.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax84k

Search PubMed and the SRA-Explorer that genomax linked. Go for the entity you are interested in. I guess you have a certain scientific question so you probably want some specific type of cancer.

ADD REPLYlink written 5 months ago by ATpoint35k
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