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Hi Developers,
I have smartseq2 data which is un-stranded, I use -s XS , but "?" appeared in my result. I read your comments before, THEN I use -s 0 ,
regtools said "Unrecognized strandness a…
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The single-end SmartSeq2 pipeline is currently expecting to get reference file information from the inputs.tsv file created in the GetInputs step. However, those fields are not included in the inputs …
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## patch-seq assay
Label: patch-seq assay
Alternative term(s): patch clamp and RNA sequencing assay
Definition: A single-cell RNA sequencing assay that takes a patch clamp recording from a cell a…
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`scripts/light_class_input.py ` expects two bam files -- one each for R1 and R2
```
python3 scripts/light_class_input.py --outpath /oak/stanford/groups/horence/Roozbeh/single_cell_project/output/m…
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The treon notebook test suite, which we fixed up yesterday, is now hanging, causing all Travis tests to fail.
This issue was not seen with the PRs yesterday that fixed the treon test harness, but t…
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Hi, I am trying to run velocyto on the SmartSeq2 data with following command
velocyto run-smartseq2 -d 1 `find ./01-genomeAligned/ -name "*.bam" -print` ~/Genomes/Mus_musculus.GRCm39.103.gtf -o…
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Trying to run velocyto with the following command:
`velocyto run-smartseq2 -o OUTPUT -e *sorted.bam gencode.vM21.annotation.gtf`
Getting following error:
```
2019-05-27 17:00:20,075 - DEBUG - …
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Hi team, congratulations! You've made remarkable and inspiring progress! And I wonder whether it would be convenient for you to upload the content about the processed Smartseq2 data since the paper ha…
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Hello,
This is more of a question than an issue, but I would like to run velocyto on bulk, 100x100 RNA-seq. I have 6 samples currently, all with >30m reads. Is there any particular way you would su…
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Hello,
I am working through the SmartSeq2 scRNA seq of Oligodendroglioma tutorial for CONICSMat and running into an issue with this part:
vg=detectVarGenes(suva_expr,500)
ts=calculateTsne(suv…