I have a 10X single cell STARsolo output BAM. And I wanna get intron junction file of only one cell. I achieved my aim by two way as below.
- I extracted a smaller BAM of specific cell Barcode and used this BAM to generate exon-exon junction counts with regtools;
- I used regtools directly with parameter ‘-b’ and the file containing the specific cell Barcode.
However,I got different output. And I found that with or without -b parameter would get almost the same output.
I wanna know why. Did I use wrong format file which containing the specific cell Barcode? If so, what is the correct format?
I have a 10X single cell STARsolo output BAM. And I wanna get intron junction file of only one cell. I achieved my aim by two way as below.
However,I got different output. And I found that with or without -b parameter would get almost the same output.
I wanna know why. Did I use wrong format file which containing the specific cell Barcode? If so, what is the correct format?