10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Dehash fastq files #214

Closed royfrancis closed 8 months ago

royfrancis commented 1 year ago

I have fastq files from a hashed 10X VDJ library that looks like this:

PBMC_1_3_1_TCR_S5_L001_I1_001.fastq.gz
PBMC_1_3_1_TCR_S5_L001_R2_001.fastq.gz
PBMC_1_3_1_TCR_S5_L002_R1_001.fastq.gz
PBMC_1_3_1_TCR_S5_L001_I2_001.fastq.gz
PBMC_1_3_1_TCR_S5_L002_I1_001.fastq.gz
PBMC_1_3_1_TCR_S5_L002_R2_001.fastq.gz
PBMC_1_3_1_TCR_S5_L001_R1_001.fastq.gz
PBMC_1_3_1_TCR_S5_L002_I2_001.fastq.gz

This is one library that has 3 samples hashed and pooled together. Is it possible to dehash these fastq files into three separate fastq files by sample? I am looking for dehashing at fastq level and not at count level.

evolvedmicrobe commented 1 year ago

This is our current recommended workflow for this.