How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode?

How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode?

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Hello everyone,

I have a sample of scRNA seq data (A.Thaliana) generated by 10X Genomics. The data is composed of R1 (cell barcodes and UMIs) and R2 (actual reads) in FASTQ format. The sample has around ~7000 cells

I ran the data through STAR solo to map them to the genome. The results are a BAM file (mapped reads) and count matrix files.

I need to run the mapped reads through some sort of an algorithm. However, if I run the produced BAM file, it will be dealt with as bulk rna-seq. So, ideally, I want to split the BAM file into a separate file for each cell. Splitting the FASTQ file would be ok too then I run them separately through STAR (not sure about the efficiency of this though).

I am working on Bash terminal environment

Is there a method to do so? Any suggestions?

I am an undergraduate student and completely new to this. Any help would be appreciated.
Thank you!!


10xgenomics


RNAseq


scRNA


CB

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