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YiPeng-Gao / scDaPars

Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
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ask for the minimum bam file numbers #19

Open zwyy5520 opened 2 years ago

zwyy5520 commented 2 years ago

Hello,

if I only have 4 bam files , can I continue to use scDapars for analysis?
when I run scDapars with 4 bam files ,the program reported the following info :

[1] "Reading in raw PDUI matrix ..." [1] "number of genes in raw count matrix 2353" [1] "number of cells in raw count matrix 8" [1] "Reading finished!" [1] "Start Processing raw PDUI matrix" [1] "Pre-Processing finished" [1] "Start Imputation Steps ..." [1] "Find potential Neighboring Cells ..." Error in RANN::nn2(t(mat_pcs), k = 30) : Cannot find more nearest neighbours than there are points

So,what changes should I make to let this program work? Looking forward to your reply. Thank you.

YiPeng-Gao commented 2 years ago

since scDaPars uses clustering first to find neighboring cell, if you only have 4 samples, it doesn't make sense to run scDaPars. You will need to create 1 bam file per cell to run scDaPars.