User: piyushjo
piyushjo • 550
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Posts by piyushjo
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... A single time point sample can also have cells from different developmental stages. For example, if you have sample of brain and you dissected region including SVZ to cortical layer, you will have the developmental stages a cell will pass through its differentiation gene. In that case a trajectory a ...
written 4 months ago by
piyushjo • 550
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... Google is your friend, unless you prefer bing. ...
written 5 months ago by
piyushjo • 550
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... It is correct that any integration method will forcefully correct the difference across population, as the intended function is to correct the "batch" effect here the "batch" effect are coming from disease.
In the present scenario, where there are samples based on treatment (healthy vs patient) co ...
written 5 months ago by
piyushjo • 550
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... Cellranger has [tutorial][1] how to make Cellranger compliant gtf from your choice of .gtf. They also mention how to convert it into premRNA gtf.
I would like to tell you that in pre-mRNA gtf, genes that are overlapped by other genes will not be counted.
For that, you should align the reads to exo ...
written 5 months ago by
piyushjo • 550
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... I will suggest using [FastMNN()][1] wrapper, also available with Seurat package, to integrate different samples. CCA, in my and others' experience performs forceful integration. It is useful only if you know all the libraries are biological/technical replicates.
[1]: https://github.com/satijala ...
written 5 months ago by
piyushjo • 550
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... > However, as I understood, these score values should not be compared
> between the different signatures because they do not have a "physical
> meaning"
This statement says that you cannot compare between two signatures, but you can still compare between clusters. For example the cell cyc ...
written 5 months ago by
piyushjo • 550
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Comment:
C: Tophat / output without XS
... Is this RNA-seq data? Any particular reason you are using tophat and not new aligners like HISAT2 or STAR?
In HISAT2 you have to specify strandness, in default condition it assumes unstranded, could be the same issue with tophat. ...
written 5 months ago by
piyushjo • 550
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... I have also used GSVA and found it to be really easy and good. Below paper also performed a comparison where GSVA was recommended, you can read for more details.
One of the way one colleague of mine has done is to combine GSVA enrichment score with gene correlation score. For correlation, you can ...
written 5 months ago by
piyushjo • 550
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... As my friend says, Because Yes :D
In reality, a lot of programs are made to run on Linux and Mac, and sometimes only Linux. While Mac is expensive (and really expensive), Linux is free, you have freedom for different distros, plus the online community can solve all your problems. I never really tri ...
written 5 months ago by
piyushjo • 550
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Comment:
C: PCA on FPKM data
... It's alright. You are the pro! I was just trying to get more information but you had better answer. ...
written 5 months ago by
piyushjo • 550
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