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After going through vignette , I wonder that should the UMI correction phased be done before or after QC ?
The `reads_per_umi_per_cell` from dropEst is already filtered. If I perform some manual fil…
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Hi VeloCytoers -
I've been trying to use this tool by following the Chromaffin tutorial with my own data. Unfortunately, I'm stumbling on the very first QC measure. The histogram of reads per gen…
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I have mapped reads from smart-seq2 experiment to a bam file for each cell (using mm10). When I am trying to estimate the necessary matrices using read.smartseq2.bams function and genes.refFlat file …
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## Bug Report
### Expected behaviour
ToolTests objects should return a URL to the underlying file
### Actual behaviour
ToolTests objects actually return a relative path as if they were par…
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I have a loom.file of 3,000 cells (from SmartSeq2). But I only want to analyze one type of about 2,000 cells.
Can I select these cells from the loom.file according to CellIDs?
Or do I have to create…
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Hi sorry if I'm missing something obvious here, but when running `run_smartseq2` is there a way of adding metadata information.
Im currently going through the API info but can find any reference t…
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Running into an error when attempting to build a viewer with sample dataset in sampleData/sample1.
Traceback (most recent call last):
File "../../src/cbBuild", line 10, in
cellbrowser.conv…
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**What problem does the suggested enhancement solve? Please describe.**
At the moment integration tests use spreadsheets checked into the test repository. This means it can become out of sync with …
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I ran this command, for SmartSeq2 data:
```
velocyto run_smartseq2 -o ./velocyto star/22606_3#7*/22606_3#7*.2pass.Aligned.sortedByCoord.dedup.bam $GTF
```
I was using a bam file with some read…
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hi! I am running this code:
==============
library(velocyto.R)
path