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The current mechanism for SS2 bundles is that each cell is in it's own bundle. This keeps the data organized in the smallest possible increments and allows the user the most flexibility. It produces t…
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Hi,
I tried using kb-python to get raw count matrices from fastq files obtained from smartseq2. I got paired end data and have two fastq files. However, I got an error telling me I need four files.…
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Hello STAR team,
Thank you for the nice tool, i use it a lot.
Currently i am trying to run STARsolo on a SMARTseq2 dataset GSE209742.
I have downloaded all the fastq files and created a manifest…
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Dear Velocyto Team,
It looks like that version `0.17.10` introduced a bug into `run_smartseq2`.
When running
`velocyto run_smartseq2 -o OUTPUT -m mm10_rmsk.gtf -e 35_rmsk ../bam-star/35/Aligned…
d-j-k updated
6 years ago
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Dear velocyto-team,
Sorry to open this issue, and I am suffering an unknown problem when I used velocyto run-smartseq2 command to operate my sorted .bam files. The command I used is as follows:
…
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Hi Sir or Madam,
I am trying to use your package, but I meet an Error as following:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/XX/opt/anaconda3/lib/python3.7/site-packages/scA…
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Dear Alex,
I am currently running the STAR pipeline (with featurecounts afterwards) for single-cell mapping with Smartseq2 data, and I was wondering it these parameters seem reasonable:
![image]…
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Participant downloaded matrix files for the pancreas dataset using the CLI, but found that the result was many matrices with 1 cell in each. This flow was not clear to the user
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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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Smartseq2 pipeline in DCP can analyze fluidigm library prep SS2 and single end SS2 data for both human and mouse.