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Having followed the wiki, I ran into an error in the meta rule, i.e. running the following:
snakemake --snakefile ~/analysis/dropseq/software/dropSeqPipe/Snakefile meta
got me this error at …
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Hi,
I cannot figure out how to fix this error:
InputFunctionException in line 5 of /rules/map.smk:
KeyError: 'the label [sample1_N706_S2_L001_MOUSE] is not in the [index]'
Wildcards:
sample=s…
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I tried the gene level summary with the dropseq data (GSE107122), which has 5 batches.
however, I got different number of genes in batches though the same gtf annotation is used:
I follow the tuto…
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In DropSeq experiments cell names are encoded by 12nt barcodes. It seems that no name check is performed when merging multiple datasets in ScanPy.
```python
>>> from collections import Counter
>…
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Such a feature would be quite useful for combing 10X/dropseq data with smartseq2 data.
Since the MNN method implicitly performs cell alignment using MNN pairs between different batches, I think the …
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Hi,
In my lab, we sequenced for the first time some libraries by using the SeqWell protocol.
Then I ran the Dropseq pipeline to get my count matrix. But, I would like to have some statistics about …
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Hi
I am trying to test SCnorm on a single cell data set from 10x genomics using the following UMIdata command:
"DataNorm
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Hi,
I am trying to run your pipeline on some DropSeq data, but I'm running into troubles in the dge script. Everything seems to work fine until all of a sudden this happens:
```
[1] "I am loadi…
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I'm trying sircel to process dropseq data. Everything seems to work except that I get a connection error to redis server, immediately after initialisation is executed. I can reproduce the error within…
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According to the Seurat Alignment tutorial, the union of the top 2k variable genes in each dataset is used for CCA.
```R
hvg.seqwell 2000
length(setdiff(tenx@var.genes,hvg.tenx))
>1272
```