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Hey, I am trying to do allele-specific expression analysis (ASE) for a few RNA seq samples ( 32 disease and 5 normal samples, unpaired unrelated). Could you suggest a pipeline/method to convert the ma…
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- [x] Remove all donwstream analyses e.g., DeSeq & PCA
- [x] change script [[count-matrix.py](http://count-matrix.py/)](http://count-matrix.py/) line 40 sep="\t" to sep = ","
- [x] switch to one s…
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Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure wa…
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Let's try to use regtools for this.
- regtools junctions-extract function: https://regtools.readthedocs.io/en/latest/commands/junctions-extract/
- parameters to specify:
- `-m 20` (should matc…
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Hi! Thanks so much for this package.
I am working some rna-seq in the maine species without genome
Your guide presents all downstream analysis example and R scripts with genome index, so how to …
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Kindly comment on this issue why you are interested in this mini-project
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To expand the MC2 data model, data type-specific metadata models should be assembled and reviewed by the community via the Request for Comments process. One strategy for implementing is as follows:
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Overlap and perform analysis as in #28
## Changes
- RNA-seq data is from literature.
- **`rna_cutoff`**: Instead of using (`lfc > 1` & `qval < 0.05`), now we only use (`lfc > 1`).
## Results d…
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Hi!
First off, thank you for this analysis tool!
I am analyzing some Perturb-Seq data and have followed the vignette. I ran Mixscale_Scatterplot and interestingly the perturbation score seems p…
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#### What analysis module should be updated and why?
Running the `sex-prediction-from-RNA-seq` module with the v13 kallisto data lead to the loss of feature names due to #474.
#### What cha…