Is it possible to isolate reads belonging to cells in a cluster of interest from the Cell Ranger BAM output file? Are reads in Cell Ranger BAM output files indexed? I want to extract reads from specific cells and align them again to the reference sequence to determine parent-of-origin-specific expression. Is this approach feasible?
•
written
by
singcell •
1 answer
Yes, in the BAM file, you can find the cell barcodes in the BAM tag "CB:Z:" which is followed by the barcode sequence.
For all cells within your cluster of interest, you'll need to curate all cell barcodes within that cluster, then use samtools view (or another tool) to extract them from your BAM file.
I believe you can use samtools view -D CB:cells.txt and then put your barcodes into a file named cells.txt (haven't tested it myself though).
Log in to answer this question.
-
Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger multi with Combined Hum…
written by tlallihuacan •
-
10X #3' RNA seq - How is strandedness determined?
written by Ashley •
-
Allele specific expression of imprinted gens from 10x scRNA-seq data
written by singcell •
-
cellranger outcome
written by Andy •
-
Extract list of mapped UMIs in cell ranger output
written by miguellarrazlopezdenovales •
-
Number of cells in each clusters
written by singcell •
-
Removing contamination of set of genes from selected cell clusters
written by singcell •
-
Gene expression values each samples (replicates) using `AverageExpression` function
written by singcell •
-
Convert 10x single cell RNA-seq bam file to bulk RNA-seq bam file
written by krc3004 •
-
Is it possible to determine if cells are clustered by samples and not by cell types?
written by singcell •
