Open emdann opened 4 years ago
Hi Emma,
Have you add the pmat
to the snap file? In order to let SnapATAC load the cell-by-peak matrix, you will need to first add the pmat
to the snap file. You can do it with the following command:
snaptools snap-add-pmat \
--snap-file /home/jovyan/my_data/cellranger-atac110_count_30439_WSSS8038360_GRCh38-1_1_0.snap \
--peak-file peaks.combined.bed
Once you add the cell-by-peak matrix into the snap file, you should be able to load the pmat by addPmatToSnap
in R.
Is there a way to export the snap object as a snap file? I am performing this analysis using 3 samples integrated together but started with three individual snap files.
Thanks
Hello, Did you solve this question? I also get this error and I perform analysis on 8 samples.
Hello, I am following the vignette for scATAC and scRNA integration and I got stuck in Step 14 (Create a cell-by-peak matrix). I used snaptools to add my cell-by-peak matrix in the snap object with
snaptools snap-add-pmat
, but when I try to add it to the R object I get the following errorDoing some debugging I figured this might have something to do with memory requirements, but I keep getting the same error if I clean everything and if I subset the data.
My dataset:
My peaks:
Any suggestions? Thanks, Emma