What is the barcode and UMI in my 10x single cell sequence data?
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8 weeks ago
Hmm • 0

Hello,

I am aiming to call somatic variants with the method of single cell RNA sequencing of sample data sets. I have a raw fastq file and will demultiplex with 'BBMAP demuxbyname code' to single cell fastq files.

I wanna know 1. which one is the barcode and UMI (in which read : 1 or 2) and 2. Which should I use among barcode and UMI to split into single cells and 3. How

My data is single end read since it is single cell data.

more details are welcomed with the real-used experienced coded.

10x singlecell RNAseq barcode demultiplex • 299 views
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My data is single end read since it is single cell data.

Hope you are referring to R2 file which contains the cDNA read. You will always have paired-end data with 10x. The first read (R1) contains the cell barcode sequence, which is 16 nt long and a UMI sequence that is 10 nt long.

While BBMap is an excellent tool you will want to use a single cell specific package like Alevin-fry or Cellranger to work with this data.

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I will try so you mean my data has barcodes like below , Read 1 of 10x which contains barcode + UMI

So, can I proceed with those barcodes (not UMI) for the index, which is required for the option of demultiplexing tool?

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Single-data analysis software will do the needful. You don't need to demultiplex this data separately.

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