User: A. Domingues
A. Domingues • 1.5k
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- Location:
- Mainz, Germany
- Website:
- http://adomingues.gith...
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- keyboardpipette
- Last seen:
- 1 day, 2 hours ago
- Joined:
- 6 years ago
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- a***********@gmail.com
Biologist doing research in gene expression regulation with a background in neurobiology and entering the world of bioinformatics.
Posts by A. Domingues
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... Hi had the **exact** same problem and eventually found the solution:
When creating the `design` object it needs a variable column which is not `Time`. My guess is that `maSigPro` was designed with multi-factorial experiments in mind, as seen in the vignette, and expects another (mock) condition oth ...
written 5 months ago by
A. Domingues • 1.5k
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... Hi Simon, did you eventually found a solution for this problem? I am running into the same issue and would appreciate some help. ...
written 5 months ago by
A. Domingues • 1.5k
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... I think this table is little outdated in relation to `bpipe` - which I use daily. SLURM support exists (at least we are using it in-house), and I am pretty sure that stages in R can be run natively without wrapping in an Rscript. ...
written 7 months ago by
A. Domingues • 1.5k
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... > Yes, that makes sense. It would be great to follow-up the work with a ChIP experiment in order to see if markers of active transcription overlap with your regions.
ChIP-seq is very very difficult because we are dealing with small number of cells (~1000), sub-population of cells during early em ...
written 8 months ago by
A. Domingues • 1.5k
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... It just might. A bit more evolved than what I had in mind, but could give out extra useful information. I look into it, cheers. ...
written 8 months ago by
A. Domingues • 1.5k
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... Thank you for the insightful comments/suggestions Kevin. Most of the questions about functionality were already in my follow-up list (and then some) and the ones that aren't is because they are not relevant to our model (non-human or mammalian). We also have a pretty good biological hypothesis, in f ...
written 8 months ago by
A. Domingues • 1.5k
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... **Background**
We observed some RNA-seq coverage in regions without annotated genes - let's called them intergenic. This expression appears to be more pronounced, or unique, to a particular condition.
**Goal**
Find those genomic regions that have higher coverage than expected by random noise alon ...
written 8 months ago by
A. Domingues • 1.5k
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... `$fasta` is a variable that represents the input fasta. It should be defined before the loop as `fasta=my_fancy.fasta` ...
written 12 months ago by
A. Domingues • 1.5k
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... If I read the question correctly I think the OP is looking for something like piRNA clusters - regions enriched for certain types of smRNA. Slightlym different approach because the regions/clusters would have variable lengths, and most of the genome would be free of these. More like a aggregation op ...
written 14 months ago by
A. Domingues • 1.5k
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... I suggests a combination of `bedtools` [merge][1] or [cluster][2], depending on what is the final goal. For instance, using `merge`:
```
## code untested
bamToBed -i my.bam \ # converts bam to bed. Ensures that read ID is kept which will be useful for counting
| mergeBed -i stdin -c 4 -o count \ ...
written 14 months ago by
A. Domingues • 1.5k
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