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MAFtools variant classes mapping
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
A: How To Merge Two Fastq.Gz Files?
Answer: Annotating file using bcftools
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Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
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I think you're misunderstanding some concepts here. WGCNA is a framework that defines modules based on how and which genes are correlated …
Comment: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
GenoMax
142k
> most up-to-date build Major build of the genome remains GRCh38. What you are looking at is the latest patch release for that build. Only…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
manuelmourato25
• 0
Thank you @atpoint . My apologies, maybe I should rephrase the question. I read the WGCNA docs already, and for the Pearson correlation tes…
Comment: How to extract cells of different species after mapping with combined genome?
by
GenoMax
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Can you confirm that this answer is specific for `singleron` technology and associated bioinformatics software.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
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GenoMax
142k
What OS are you using? Are you able to run `blastn --help` and does it produce the in-line help? > I used many query file.fasta And tho…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
82k
> However, even though 3 biological replicates per condition seems to be the norm in these experiments, many papers discuss that we need at…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
ATpoint
82k
> I have curiosity, why do you make a desing with interceptor and without contrast matrix? Because for a 2-group comparison you do not nee…
Comment: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
ATpoint
82k
If you have a one-click workflow ready and the necessary computation power to casually run it, then go for it. If it is any greater effort …
Comment: Seurat v5 and how to correctly integrate across multiple experiments
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Papyrus
★ 2.9k
In my experience integration methods are also often used for different samples/batches across the same technology. The crucial thing is to …
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much! I have repeated the code adding arrayWeights() and it's works! In this case, I have a desing without intercept and c…
Comment: Is there any way to modify this pie chart ?
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ohtang7
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Thank you, I've tried but I see only some appear in the chart in wrong segments. Could you help me to solve this how ? ![enter image desc…
Comment: perseus software (version 1.5.5)
by
DGTool
▴ 10
If the tool mentioned relates to the Perseus application from the Cox lab ([here][1]), it should be free to download after accepting the li…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
DGTool
▴ 10
At least so far to my knowledge, I don't think it would be worth re-mapping to GRCh38.p14, if it is too much trouble or with what you're lo…
Answer: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
From the marker genes of each cluster, we can determine whether the cluster belongs to human or mouse. Human genes are all capitalized, whi…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
Thanks a lot. It is almost what I need but not all. From your script, I can get information that how much degree different samples contri…
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