@alexdobin I am trying to use the data from this paper. The preparation kit used for the snRNA-seq data was MGI's DNBelab C series kit. I am specifically trying to look at the brain tissue samples. I have downloaded the fastq files from NCBI with parallel-fastq-dump and split them into R1 and R2. R1 contains the barcode and UMI information. I found the barcode structure here which states that there are barcodes in R1 from position 1-10 , then another barcode from position 11-20, and finally the UMI is position 21-30. The paper does not document the alignment code, but said it uses Cellranger (version 6.1.2) to align the samples. They also say that R1 has read length of 30bp and R2 has 100bp. I'm confused on how to use the barcode list they provide, do I create all combinations of positions 1-10 with 11-20 into a single barcode list file? Any information on how to align these samples would be helpful for me.
@alexdobin I am trying to use the data from this paper. The preparation kit used for the snRNA-seq data was MGI's DNBelab C series kit. I am specifically trying to look at the brain tissue samples. I have downloaded the fastq files from NCBI with
parallel-fastq-dumpand split them into R1 and R2. R1 contains the barcode and UMI information. I found the barcode structure here which states that there are barcodes in R1 from position 1-10 , then another barcode from position 11-20, and finally the UMI is position 21-30. The paper does not document the alignment code, but said it uses Cellranger (version 6.1.2) to align the samples. They also say that R1 has read length of 30bp and R2 has 100bp. I'm confused on how to use the barcode list they provide, do I create all combinations of positions 1-10 with 11-20 into a single barcode list file? Any information on how to align these samples would be helpful for me.