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oops. Me again! So the slopper pipeline finished with my data, but I got an error message in `SL.featureCounts.genes.log.txt`:
```
Error in min(Y) >= 0 :
only defined on a data frame with all…
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* spladder version: latest
* Python version: 3.6
* Operating System: linux-ubuntu
Hi,
With the produced read counts, for A3/A5 and RI, it is eazy to speculate that PSI=intron_conf2/(intron_co…
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Hi,
I have performed HISAT2 Stringtie and ballgown pipeline and reached till end with my own data.
while using isoformswitchanalyzer, I am facing problem.
proble:
salmonQuant
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Hi all,
I am using CRISPResso2 and I would like to add the option to ignore substitutions. However, whenever I try adding it to the script it encounters an error and I don't get any output. I have …
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I'm still having numerous issues with the fibroblast data from the [Smart-seq3 paper](https://doi.org/10.1038/s41587-020-0497-0), downloaded via [ArrayExpress](https://www.ebi.ac.uk/arrayexpress/exper…
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Hi all,
I have two basic questions if I can apply scvelo on my data set. We have generated single cell **nuclei** data (not cell) - extracting the cell nuclei without the cytoplasm. So in principle…
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I have added gene_name s to the original Refseq genome annotation file from UCSC, but when I run Stringtie and Ballgown, there are some genes/transcripts that don't have their gene_name added and only…
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Hi!
Me again... I'm running sloppr on my dataset but realized my gff does not have 'exon' attribute. Here is what my gff looks like:
```
Monodopsis_C73_contig_1 AUGUSTUS mRNA 18365 …
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Hi Sebastian,
In our tasks after the detection of the let say Gene1-Gene2 fusion,
we are usually interested whether the wild type Gene1 and Gene2 are also expressed.
So we need to somehow quantif…
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Docker is running though... below is the full log
```
Command executing: Powershell.exe docker pull smithlab/spritz ;docker run --rm -i -t --name spritz-956943642 -v """Z:\AGS\AGS RNAseq CNIO\raw da…