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Question about single cell regtools junctions extract. #182

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xiaohe0404 opened this issue Mar 13, 2024 · 0 comments

xiaohe0404 commented Mar 13, 2024

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?

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