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Hello,
currently, I am trying to run IsoformSwitchAnaylzer with Kallisto counts. After successfully using importIsoformExpression() to extract my count data, I wanted to set up the switchAnalyzeRlis…
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Hi, I noticed that your default output annotation is an extended annotation(reference+novel). While I want to get the annotation that assemble from the RNA-seq data. That is, I want to get the transcr…
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Hi B,
I'm trying to generate the pca and from doing salmon i have a gene.counts.matrix and an isoform.counts.matrix.
im trying to execute
% $TRINITY_HOME/Analysis/DifferentialExpression/Pt…
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Dear Alex Dobin.
First of all, thanks for this fantastic tool and all your work during these years to update it.
Recently some colleagues attended the conference Biological Data Science 2022 and…
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I'm currently working on setting up a simple RNA-seq analysis pipeline using snakemake, and I've integrated the STAR wrapper from snakemake-wrappers. However, I've run into an issue where specifying `…
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Hello,
I'm using IsoformSwitchAnalyzeR version 2.1.2 and I'm having some trouble importing the data using importRdata. My data comes from Isoquant and I'm using both counts and tpm tables.
```…
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**Describe the bug**
Hello, thanks a lot for the very useful tool. I am trying it for the first time and I am starting from the already analyzed Seurat object.
I am importing and transforming the gt…
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Here is my running code:
```
time metawrap quant_bins -b temp/bin_refinement2/ref4/metawrap_70_5_bins/ \
-t 48 -o temp/bin_arg/quant/summer \
-a result/megahit/summer.contigs.fa \
tem…
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Hi,
I am trying the tool for the quantification of nuclear RNA, after my recent tweets with Lior Patcher.
Every commands in the Velocity tutorial seems to work, but I want only the quantificatio…
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A lot of the times when we are assessing our samples before we move on to fragmenting cDNA in to fragments, we look at the distribution of full length cDNA using a Bioanalyzer.
See for example panel …