Moderator: Bastien Hervé
Bastien Hervé ♦ 4.8k
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- Karolinska Institutet, Sweden
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Posts by Bastien Hervé
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... The error is clear :
awk: cmd. line:1: {print $1" "$2" "$3" "$4"}
awk: cmd. line:1: ^ unterminated string
The `"` after `$4` should be remove
Tabulation is a better delimiter than white spaces
awk -F '\t' '{print $1"\t"$2"\t"$3"\t"$4}' myfile.map > myfile_f ...
written 3 days ago by
Bastien Hervé ♦ 4.8k
2
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2
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140
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... After one week on this matter I think it is time to know when to stop digging. Here is where I went so far :
https://gist.github.com/Baboon61/4a8dc2e2e433432615a5ba8bae06f249
----------
https://gist.github.com/Baboon61/69afb6e94c41af05d81b16c85e793dab
You can notice that both objects before `SCT ...
written 4 days ago by
Bastien Hervé ♦ 4.8k
0
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52
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Comment:
C: What next after gene list?
... Hello, you can highligth the top ones ...
written 5 days ago by
Bastien Hervé ♦ 4.8k
0
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2
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140
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2
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... apply10SCTransform.HOME = list()
apply10SCTransform.HOME <- mclapply(1:10, function(i) {
SCTransform(SCRNARR.HOME, seed.use=1447854, variable.features.n = 2000, vars.to.regress = "percent.mt", verbose = FALSE)
})
for (n in 1:9){
print(setdiff(rownames(apply10SCTransform. ...
written 10 days ago by
Bastien Hervé ♦ 4.8k
0
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2
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140
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2
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... Yeah the objects are the same size every time at the lab and every time the same size at home but objects size are different from the lab compare to the ones I get from home.
mclapply(1:10, function(i) {
object.size(SCTransform(SCRNARR.LAB, seed.use=1447854, variable.features.n = 2000, va ...
written 11 days ago by
Bastien Hervé ♦ 4.8k
0
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2
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140
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... Thank you, really interesting thinking ! I dug a bit more into SCTransform and seems like the HVGs are not always the same, see below.
Warnings are the same in both cases, the same line is repeated except for warning 31 :
#Warnings
29: In theta.ml(y = y, mu = fit$fitted) : iteration limit ...
written 11 days ago by
Bastien Hervé ♦ 4.8k
5
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2
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140
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... Due to Covid19 situation I am working part time at the lab and at home. At the lab I am working under an HP workstation linux environment and at home on MSI with windows 10 and Rstudio.
As input to the SCTransform function I use the same RDS object, same parameters, same R version, same Seurat vers ...
written 12 days ago by
Bastien Hervé ♦ 4.8k
0
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0
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115
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... You have a `label.size` option in the `DimPlot` function. Type `DimPlot R` on google to have the documentation of every R function. Please show some more effort of trying in your future questions.
https://www.rdocumentation.org/packages/Seurat/versions/2.3.2/topics/DimPlot ...
written 27 days ago by
Bastien Hervé ♦ 4.8k
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95
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... Hi, I think you can do that with [Entrez][1]
[1]: https://cran.r-project.org/web/packages/rentrez/vignettes/rentrez_tutorial.html ...
written 28 days ago by
Bastien Hervé ♦ 4.8k
0
votes
1
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150
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1
answers
Comment:
C: RNASeq, gtf file
... You can do that in Bash or Python for example. Here are the steps :
- Select "transcript" lines
- Split by ";"
- Look for element starting with "FPKM"
- Once found, compare FPKM value to 2.
- Keep the line if higher than 2 ...
written 4 weeks ago by
Bastien Hervé ♦ 4.8k
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