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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Question about Cell line analysis #168

Open Qingrun opened 4 years ago

Qingrun commented 4 years ago

HI Fang,

I am analyzing two different cell lines, each cell line have the wild type and Knock out subtypes. All the 4 samples are sent to 10x scATACseq at the same time. I walked through all your examples, but still feel that my case is a bit different.

  1. Since I have a specific type of cultured cells to sequence, the cluster in each type of cell seems to provide information for the heterogeneity status of the cell. I can compare the differential accessibility of clusters in each type of cell to study the different status.
  2. When it comes to differential accessibility analysis for wild type vs knock out cell lines, how to merge the clusters in each cell line?
  3. At the step of creating a cell-by-peak matrix, and add to snap file, since I have 4 snap fil, but one peaks.combines.bed file, should I to each snap file?
  4. At step of adding cell-by-peak matrix to snap object, table(x.sp@sample) has 4 types of sample. How should I add all the *.snap.rds files by readRDA? Can it read multiple files in? 5.How does DAR(differential accessible regions) defined? For example, in a cluster, who does this cluster compared with to get DAR?

Thanks. Qingrun

singcell commented 3 years ago

@Qingrun Did you figure it out? I am in similar situation.