Gene Tracks from 10x Data

Question

[ntsopoul]

hi, I am interested in the 3’ UTR of genes and would like to see the gene tracks of certain populations. How can I extract from 10x data e.g. bam files the specific cell population and make bigwig files out of this subset? Is there a tool where I can inspect a bam file, select a population from reduced dim plots and visualize the gene tracks? I could not find such a function with the loupe browser for rna-seq. However the loupe browser can do it for atac-seq …

Answer 1

[swbarnes2]

The bams that 10xGenomics makes are tagged with cell barcode. So figure out which call barcodes you want, then you can filter the bam accordingly.

I don't know off the top of my head if you can get cell barcodes out of Loupe. You might need to use something like Seurat.

[ntsopoul]

Thanks a lot! I thought already that something similar might be the case... So by filtering you mean "grep" the cell ID of interest from the .bam file into a new .bam file

It is just sad that there is no tool to inspect the tracks of cells. It will be a pain to do this ...

[LChart]

IGV

right click reads -> Experiment Type -> RNA

this will split reads out by the "CB" tag for you.

This won't generate .wig files for you; but filtering by a read tag (instead of a read FLAG) would be a great feature request for deeptools (https://github.com/deeptools/deepTools)

[swbarnes2]

Yeah, pretty much. Possibly Picardtools has something for filtering by tags?