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Recent Replies
Comment: database of cancer and normal cell lines
by
yueli7
▴
250
Hello GenoMax,
Thank you so much for your great help!
I really appreciated!
Best,
Yue
Comment: How to Handle Incorrect Clade Grouping of a Reference Genome in a Phylogenetic T
by
oasiswho
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0
Dear Mensur Dlakic
Thank you very much for your response. I am currently working on constructing a phylogenetic tree based on mitochondrial…
Comment: Detecting genomic signatures of drug resistance breast cancer in transcriptomic
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DareDevil
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4.3k
You can contact me biologsr[at]gmail.com
Answer: How to Handle Incorrect Clade Grouping of a Reference Genome in a Phylogenetic T
by
Mensur Dlakic
★
28k
> Has anyone experienced a similar issue?
I am sure many people have gotten the trees they didn't expect.
Assuming you know how to do…
Comment: Is this featureCounts output normal, and how can I process it for DESeq2 analysi
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Gordon Smyth
★
7.7k
I can read 50MB files into R in a few seconds on my laptop. Is your R session very short on memory?
Anyway, you can undertake a DE analysi…
Comment: Is this featureCounts output normal, and how can I process it for DESeq2 analysi
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DdogBoss
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I will give edgeR a go to see if the resulting feature counts file is easier to handle than in bash.
When I try to import the current fea…
Answer: Is this featureCounts output normal, and how can I process it for DESeq2 analysi
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Gordon Smyth
★
7.7k
Yes, that is normal output.
Have you considered using the simpler R-based interface:
```
library(Rsubread)
library(edgeR)
files <- c("samp…
Answer: Iterative clustering with silhouette score
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Mensur Dlakic
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You didn't tell us what type of clustering is used here. Specifically, how do you determine the number of clusters?
With the information…
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GenoMax
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How did you make your `salmon` index? Using the transcript file for v.46 from GENCODE?
<!-- this is it -->
Comment: database of cancer and normal cell lines
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GenoMax
147k
See
https://www.proteinatlas.org/humanproteome/cell+line<br>
https://gtexportal.org/home/aboutAdultGtex<br>
http://gent2.appex.kr/gent2/<b…
Comment: Gene locus and gene ID
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`ENSG00000260958` is marked as a novel transcript based on [**HAVANA**][1] (manual) analysis. It is overlapping several other items that ar…
Comment: Gene locus and gene ID
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zizigolu
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Actually my question is why when IA search for `ENSG00000260958`, these three `TP53TG3GP`, `RARRES2P5` and `FGFR3P5` comes? Does this mean …
Comment: Estimate error-rate and assembly oftion for FLYE assembler
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If data has been basecalled with `dorado` using super accuracy (SUP) or high accuracy (HAC) models then use the `--nano-hq`.
Comment: Estimate error-rate and assembly oftion for FLYE assembler
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Umer
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Thank you for clerification.
based on my Raw data i get error rates around 2–2.2%.
Shold i use `--nano-hq` or `--nano-raw`.
what do you …
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