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Hi,
I am very interested in using Dendro for my scRNA-seq dataset which was generated using plate-based Celseq2 method.
I have 4 different conditions, each 3 plates of 384 cells. How does the cell identification work within the pipeline? Do I need to make a separate VCF file per cell?
Thank you very much for your answer.
Cheers,
Dyah
The text was updated successfully, but these errors were encountered:
Sorry I am not very familiar with plate-based Celseq2. Does it have barcode? Could you separate their reads with barcode to individual BAM files? Our gvcf pipeline take advantage of large computing clusters by run separate mutation detections in individual cells in each core and then combine them together. Running with all cell combined can take monthes to run (from my own experience...)
Hi,
Yes, it has cell barcode. The read 1 consists of 8 bp UMI and 8 bp cell
barcode, which is used to repared reads to individual fastq and then, SAM
files.
On Thu, Dec 10, 2020 at 6:34 AM Zilu Zhou ***@***.***> wrote:
Hey Dyah,
Sorry I am not very familiar with plate-based Celseq2. Does it have
barcode? Could you separate their reads with barcode to individual BAM
files? Our gvcf pipeline take advantage of large computing clusters by run
separate mutation detections in individual cells in each core and then
combine them together. Running with all cell combined can take monthes to
run (from my own experience...)
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Hi,
I am very interested in using Dendro for my scRNA-seq dataset which was generated using plate-based Celseq2 method.
I have 4 different conditions, each 3 plates of 384 cells. How does the cell identification work within the pipeline? Do I need to make a separate VCF file per cell?
Thank you very much for your answer.
Cheers,
Dyah
The text was updated successfully, but these errors were encountered: