User: VHahaut
VHahaut • 990
- Reputation:
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- Vincent_Hahaut
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- 2 years, 3 months ago
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Posts by VHahaut
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... You might have to give a bit more details about your code, package used, example, ... This is not enough to allow us to help you. ...
written 5 days ago by
VHahaut • 990
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198
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Comment:
C: range of fold change in RNA seq
... Have they been sequenced at the same time? Are the coverages roughly similar (size factors?) ? ...
written 10 days ago by
VHahaut • 990
1
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1
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128
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1
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Comment:
C: Stack several manhattan plots
... Using the facet_wrap you'll split your graph in as many chromosome as you have:
library(dplyr)
library(ggplot2)
tmp <- data_frame(
CHR=paste0("chr", sample(1:10, 1000, replace=T)),
POS=seq(1,1000),
pval1=1/runif(n = 1000, min=0, max=0.2),
pval2=1/c(runif( ...
written 12 days ago by
VHahaut • 990
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Answer:
A: Stack several manhattan plots
... With a bit of customization you could do it in R with ggplot:
library(dplyr)
library(ggplot2)
tmp <- data_frame(
POS=seq(1,10000),
pval1=1/runif(n = 10000, min=0, max=0.2),
pval2=1/c(runif(n = 9999, min=0, max=0.2), 1e-5),
pval3=1/runif(n = 10000, min=0, ...
written 12 days ago by
VHahaut • 990
1
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1
answer
136
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1
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Answer:
C: data frame from deseq2
... Ok so you mean you want to save it as a text file somewhere?
write.table(assay(rld[res.index,]), sep="\t", path, row.names=F, quote=F)
where `path` should be replaced by the full path where you want to save it such as:
write.table(assay(rld[res.index,]), sep="\t", "~/Desktop/rld_norma ...
written 24 days ago by
VHahaut • 990
1
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1
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136
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1
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Comment:
C: data frame from deseq2
... Do you mean the rld normalized count table?
assay(rld[res.index,] ...
written 25 days ago by
VHahaut • 990
3
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2
answers
133
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2
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... There are all paralogues:
[http://www.ensembl.org/Homo_sapiens/Gene/Compara_Paralog?db=core;g=ENSG00000284332;r=1:30366-30503;t=ENST00000607096][1]
[1]: http://www.ensembl.org/Homo_sapiens/Gene/Compara_Paralog?db=core;g=ENSG00000284332;r=1:30366-30503;t=ENST00000607096
...
written 26 days ago by
VHahaut • 990
0
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1
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127
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1
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... [https://www.rdocumentation.org/packages/Rsamtools/versions/1.24.0/topics/ScanBamParam][1]
This doesn't answer 100% your question but ScanBamParam() / ScanBamFlag can parse a SAM file and extract reads with certain features (isProperPair, isPaired, ...)
[1]: https://www.rdocumentation.org/packa ...
written 29 days ago by
VHahaut • 990
1
vote
1
answer
136
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1
answers
... write.table(results, "/path/to/your/file.txt", sep="\t", quote=F, row.names=F) ...
written 4 weeks ago by
VHahaut • 990
1
vote
1
answer
136
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1
answers
... 1. Create a vector with your sample IDs:
ids <- c("ID1", "ID2", ... , "IDn")
NB: This can maybe be obtained elsewhere. If you have a dataframe that contain all the IDs in one column you could load this dataframe and extract the IDs:
data <- read.table("file", sep="\t", header=T)
...
written 4 weeks ago by
VHahaut • 990
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12 days ago,
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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12 days ago,
created an answer that has been accepted.
For A: miRNA corresponds to multiple ensembl gene IDs
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For DESeq2 analysis: huge number of outliers and refitting
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26 days ago,
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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For DESeq2 analysis: huge number of outliers and refitting
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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For C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
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For C: Is going back to the wet lab worth it?
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For DESeq2 analysis: huge number of outliers and refitting
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For MA plots DESeq: strange MA plots
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