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4.3 years ago
ee.mohseni.alert
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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.
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?
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?
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?
You could look for papers that use a package like
sciclone( https://github.com/genome/sciclone ). Possible search example.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.
CO8 and CO5 are two different individuals sample, where:
BioSample: SAMN04893778; Sample name: CO8; SRA: SRS1419894
BioSample: SAMN04893766; Sample name: CO5; SRA: SRS1419893
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.