Moderator: Bastien Hervé
Bastien Hervé ♦ 4.9k
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- Karolinska Institutet, Sweden
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- 15 hours ago
- Joined:
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Posts by Bastien Hervé
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... Seems like no option is available for downloading a list of biomarkers.
You can still asked them about their API : https://www.mycancergenome.org/content/page/legal-policies-licensing/ ...
written 1 day ago by
Bastien Hervé ♦ 4.9k
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... You cannot do that before alignment, you have to know where a read fits the best before filtering it out or not. For mitochondrial hits you can use `samtools` to remove reads falling into chrM. For all other kind of repeat events, I believe they will be considered as multimapped. Take a look at [sam ...
written 1 day ago by
Bastien Hervé ♦ 4.9k
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167
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1
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... What is the output of `library(DESeq2)` ?
Is it loading without any error ? ...
written 10 weeks ago by
Bastien Hervé ♦ 4.9k
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... Seems like there is no `HapMap` package on pypi.org
https://pypi.org/search/?q=Hapmap
Have a look : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040524/ ...
written 10 weeks ago by
Bastien Hervé ♦ 4.9k
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... Try to upgrade pip
curl https://bootstrap.pypa.io/get-pip.py | python
What are your python and pip version ?
https://stackoverflow.com/questions/49748063/pip-install-fails-for-every-package-could-not-find-a-version-that-satisfies
https://github.com/tensorflow/tensorflow/issues/39130 ...
written 10 weeks ago by
Bastien Hervé ♦ 4.9k
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Comment:
C: Star RNA seq aligner issue:
... We do not have your STAR command line but you can try to reduce the number of thread used and increase the ulimit even more. You can also sort your BAM file afterwards. ...
written 10 weeks ago by
Bastien Hervé ♦ 4.9k
0
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0
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143
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Comment:
C: Star RNA seq aligner issue:
... Did you try what's written in SOLUTION or is it your attempts ? ...
written 11 weeks ago by
Bastien Hervé ♦ 4.9k
3
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1
answer
406
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answers
... You can try this :
library(Biostrings)
sts.data <- c(
"TTATAG",
"AGATAT",
"AGATAG",
"ATATCT",
"AGATAG",
"AGATAG",
"AGATAG",
"TGATAA",
"AGATAA",
"AGATAA",
"CGATAG",
...
written 3 months ago by
Bastien Hervé ♦ 4.9k
0
votes
1
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406
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... You cannot access `A`, `C`, `G`, `T` as you do
`seqstatd(seq1)` outputs a list of element, you need to grab the "State frequencies" informations
Try to run only these lines :
seq1 <- seqdef(seqdecomp(sts.data,sep=''))
seqstatd(seq1)
t1<-c(A)
You will see that `t1` is empty beca ...
written 3 months ago by
Bastien Hervé ♦ 4.9k
1
vote
1
answer
406
views
1
answers
... Are `A`, `C`, `G`, `T` variables or characters :
d <-c(A, C, G, T)
If they are variables, they are not in your script.
If they are characters, you cannot divide characters matrix by float values here :
makepssm <-pwm/bg ...
written 3 months ago by
Bastien Hervé ♦ 4.9k
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