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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Error in addBmatToSnap.default #186

Closed chemistmarsy closed 4 years ago

chemistmarsy commented 4 years ago

Hi Rongxin,

Thanks for your great package, it made my life much easier analysing my scATAC dataset. However I met some trouble merging two batches of sequencing data in the step of addBmatToSnap.

The two batches of data, first batch contains 2 samples, and the second one contains 8 samples. They were sequenced in 2 different sequencers in different time, but they're from the same species of course.

While I run addBmatToSnap in R merging the 10 samples, I got error like: Error in addBmatToSnap.default(x.sp, bin.size = 5000) : bins does not match between snap files, please regenerate the cell-by-bin matrix by snaptools I can make sure that they have the same bin sizes (confirmed with showBinSizes), and used exactly the same method to generate snap files from cellranger output.

The weird thing is that I have no problem merging the 2 samples in batch 1 only, or merging the 8 samples in batch 2, no errors. But once merging between batches, the error message pops up. This made me make sure the file quality is good, but the error confused me more.

I would appreciate it if you could help me to figure out what happened, like is this caused by my data quality or running the pipeline with some mistakes. Thank you so much!

chemistmarsy commented 4 years ago

This issue was solved by re-running the cellranger atac. The 2 samples in batch 1 was run by my lab mate. I believe there're some subtle differences we made in cellranger.