User: b.nota
b.nota • 3.9k
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Posts by b.nota
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... There is a nice review in [Plos Comp][1] about the different methods that are available for pathway of GO analysis. The methods (with only a list of significant genes) you are referring to are first generation. There are also second and even third generation. Read it in the paper, and you'll know wh ...
written 1 day ago by
b.nota • 3.9k
0
votes
1
answer
99
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1
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... Check [here][1] for the difference between blast and blat, and see what suits your data. I would use (stand alone) blast in this case.
[1]: http://www.ensembl.org/Help/Faq?id=429 ...
written 1 day ago by
b.nota • 3.9k
5
votes
3
answers
231
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3
answers
... The question is also duplicate
https://www.biostars.org/p/62988/ ...
written 3 days ago by
b.nota • 3.9k
0
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1
answer
148
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1
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... Are you sure such an approach will be publishable? ...
written 3 days ago by
b.nota • 3.9k
3
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4
answers
149
views
4
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... You can use `merge` with `all.x=F` and `all.y=F` arguments.
Something like:
firstMerge <- merge(df1, df2, all.x=F, all.y=F)
secondMerge <- merge(firstMerge, df3, all.x=F, all.y=F)
...
written 3 days ago by
b.nota • 3.9k
1
vote
1
answer
148
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1
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... I think that sounds more feasible, the lasso selected features for e.g. KNN or other ML method. Take a training and test set into account. Survival is another option, it depends on your research question (can you divide patient with/without MYC amplification by gene expression profile, or the other ...
written 4 days ago by
b.nota • 3.9k
0
votes
1
answer
148
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1
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... I am not sure if I understand your approach, did you find it somewhere in literature or came up with it yourself? It looks to me like you are mixing up two things, 1) machine learning, 2) limma roast.
With machine learning, you select a set of genes (also called feature selection), and then with a ...
written 4 days ago by
b.nota • 3.9k
1
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2
answers
81
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2
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... There are more tools available, I tried a few and had a good experience with R (CRAN) package [ExomeDepth][1].
[1]: https://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf ...
written 4 days ago by
b.nota • 3.9k
1
vote
1
answer
57
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1
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... You only need the bed file produced by macs2 for homer. They need to contain the coordinates of the peaks (chr, start, end position), followed by the peak name (which is given by macs2).
The output will indeed only contain "+" for each peak. ...
written 4 days ago by
b.nota • 3.9k
2
votes
3
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100
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3
answers
... It should be in the same line following `CL:`, right after the `VN:` (which is the version of bwa). The info is thus not in your files.
Here an example of a file I used:
samtools view -H SRR1291026.bwa.bam | grep "bwa"
@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem -t 20 /home/ ...
written 5 days ago by
b.nota • 3.9k
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