What is the barcode and UMI in my 10x single cell sequence data?
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Is there any tutorial page that tells you how to extract read count from illumina single-cell RNAse…
written by Simon Ahn •
-
Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq)
written by Evan •
-
Queries on 10x sequencing 3' Read 1
written by Cheng Wei •
-
Demultiplexing 10x fastq files by GROUPS of barcodes
written by bds1217 •
-
Demultiplexing single cell RNA-Seq data
written by Neu •
-
Demultiplexing and deduplicating using barcodes and UMIs in the "mate" read
written by lech.kaczmarczyk •
-
How to append the cell barcode and UMI information to the fastq header in paired-end single-cell RN…
written by sc243 •
-
Demultiplexing Conceptual Issue
written by asyndeton17 •
-
Tools for demultiplexing a large fastq file based on random in-line barcodes
written by alyssamolinaro91 •
-
Get Single Cell RNAseq DGE matrix
written by xuyang_dami •
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.
I will try so you mean my data has barcodes like below ,
So, can I proceed with those barcodes (not UMI) for the index, which is required for the option of demultiplexing tool?
Single-data analysis software will do the needful. You don't need to demultiplex this data separately.