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Recent Replies

Comment: Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
by
saipra003
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10

Thank you this makes much more sense!

Answer: Help with PCA plot from SNPRelate
by
elielsonveloso
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0

> I don't know how many you were expecting, but there are two groups of points.
I am expecting 2 groups, indeed (cases and controls)!!

Answer: Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
by
Rob
5.3k

To be clear, enabling bootstrapping or Gibbs sampling does not change the “primary estimate” (i.e. the `TPM` or `NumReads` in the `quant.sf…

Answer: Help with PCA plot from SNPRelate
by
elielsonveloso
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0

Thank you Mr. Dlakic!
I agree with your point regarding the low data variance explained by the top 2 PCs. Since I am working on a geneti…

Answer: correct list of capture targets/intervals for SureSelect mouse exome to perform
by
heskett
▴
90

hi there. having this exact problem now. what does correct chains mean? i do worry that liftover wont be entirely accurate

Comment: Help with PCA plot from SNPRelate
by
Mensur Dlakic
★
19k

You may get some idea as to what kind of separation can be obtained from t-SNE compared to PCA from the following notebook:
https://colab.…

Comment: Using fastq-mcf tool
by
aranyak111
•
0

Thanks for all the comments. I have been able to solve the problem by finding the right program execution.

Answer: Help with PCA plot from SNPRelate
by
Mensur Dlakic
★
19k

> Would anyone help me to understand my output figures? What can one conclude from such a "non-grouped" PCA plot in terms of population str…

Answer: Infinium MethylationEPIC Annotation under hg38
by
Molin
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0

It turns out that the hg38 manifest file, it provides location information based on the 0-ordinates system which means it starts from 0 a…

Answer: Illumina EPIC array manifest file header
by
Molin
•
0

Hi,
I have the same question and I just figured it out recently. it turns out that for the hg38 manifest file, it provides location inform…

Answer: Build canine dna.primary_assembly.fa for kb ref
by
Candice
•
0

I've found the answer. It turns out the Readme in Ensemble says "If the primary assembly file is not present, that indicates that there are…

Comment: Difference in total gene counts between samples
by
bart
▴
20

So to be clear, library size is not a factor which can explain the lack of correct clustering in my pcaplots right? So could I use SVA or R…

Comment: What is Nanopore Barcode Score and how is it calculated?
by
henry-keen
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20

I have the same question. Have you figured out this problem?

Comment: Htseq-count: Problem with feature counts
by
Istvan Albert
93k

perhaps the chromosome naming differs `1` vs `chr1`

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