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YiPeng-Gao / scDaPars

Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
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10x data #10

Closed Lianqw closed 3 years ago

Lianqw commented 3 years ago

Hello! For 10x example data,I want to know which GSMs in GEO132044 you used in scDapars, because there are too many samples in GEO132044.

YiPeng-Gao commented 3 years ago

Human PBMCs GSM3837156, GSM3837157, GSM3837158, GSM3837159, GSM3837170, GSM3837171, GSM3837172, GSM3837173.

YiPeng-Gao commented 3 years ago

If you open the SRA run selector, you can choose filters: 10X chromium (V2), homo sapiens, female to get the GSM.

Lianqw commented 3 years ago

There are 8 GSMs, then I want to know if you use cellranger count to process 8 SRRs at once? Or use cellranger count separately ?

YiPeng-Gao commented 3 years ago

No, you combine the first 4 as read 1 and the remaining 4 as read 2 before cell ranger.