VCF file preparation for plate-based scRNA-seq

[dwkarjosukarso]

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

[zhouzilu]

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...)

[dwkarjosukarso]

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.

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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...) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCN5BQTOSHGS2JAJVDFC4LSUBMW7ANCNFSM4SSPKLXA> .