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zhouzilu / DENDRO

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing
GNU General Public License v3.0
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VCF file preparation for plate-based scRNA-seq #13

Open dwkarjosukarso opened 3 years ago

dwkarjosukarso commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 notifications@github.com 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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