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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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multiple samples analysis: how to merge barcode files? #158

Open billzt opened 4 years ago

billzt commented 4 years ago

In FAQ it writes the following codes to start multiple samples analysis:

> file.list = c("atac_v1_pbmc_5k.snap", "atac_v1_pbmc_10k.snap");
> sample.list = c("pbmc.5k", "pbmc.10k");
> x.sp = createSnap(file=file.list, sample=sample.list);

However the next step is barcode:

> barcodes = read.csv(
    "atac_v1_pbmc_5k_singlecell.csv",
    head=TRUE
  );

Since I'll have two separated barcode files called atac_v1_pbmc_5k_singlecell.csv and atac_v1_pbmc_10k_singlecell.csv`, How to deal with them?

Rawansw commented 4 years ago

same need!

billzt commented 4 years ago

I guess it might be possible to follow https://github.com/r3fang/SnapATAC/blob/master/examples/10X_PBMC_15K/README.md

However still hope author's comments, since the 10X_PBMC_15K example is slightly different from the FAQ