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Hi there,
I have a question about the following Kallisto code: is it appropriate for generating index and reference files for single nuclear DropSeq?
“kb ref -i index.idx -g t2g.txt -f1 cdna.f…
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# Status
| Dataset | platform | fastq downloaded | samples.csv | fastq renamed/ concatenated | config.yml | pipeline success |
|--|--|--|--|--|--|--|
|zheng_zhang_2017 | smartseq2 | wait for EGA …
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Hi,
I was skimming through some of the code and other open issues on support for other library (cell barcode/umi) designs. It looks like there is code for supporting inDrop libraries, but I wasn't su…
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Can you please link the fasta and gtf files that are used when "hg19" is entered as the 'reference' input?
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Hi dropseqpipers,
I have downsampled some single cell data to test for the quality of the results using the same number of reads per cell. I have given each of my 100 cells 10,000 reads in the fa…
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Hi! I'm trying to understand some (mostly minor) differences between expression as measured by the DropSeq toolkit (of which I'm the author) and STARSolo expression outputs as we evaluate the [Optimu…
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Hi,
I am having trouble trying to follow the tutorial (http://velocyto.org/velocyto.py/tutorial/cli.html#run-dropest-run-on-dropseq-indrops-and-other-techniques).
The data I was working with were pr…
bxxu updated
7 months ago
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### NullPointerException reading BCF
I have a VCF with a single variant line in it ([buggy.vcf.txt](https://github.com/samtools/htsjdk/files/2010728/buggy.vcf.txt) _Note that .txt extension should be…
alecw updated
5 years ago
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Hi, I follow the instruction in the tutorial in order to produce the loom file for scVelo. but when I run the velocyto tools dropest-bc-correct, it reports tag "CB" is not present in the bam file. Co…
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Hi,
thank you for this great tool.
I am running spacemake for an openST data and encountering the following Error when running `spacemake run --cores 8`:
```Error
KeyError in line 286 of /ho…