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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
124 stars 11 forks source link

application in scATAC-seq data #26

Closed zhijunyuu closed 2 years ago

zhijunyuu commented 2 years ago

Hey,

Thanks for this nice tool!

I used the cellsnp-lite and vireo for demultiplexing some 10X Genomics single cell RNA-seq data, it worked very well. Based on the description of cellsnp-lite, I think it could also be used on scATAC data. So I tried to use cellsnp-lite on some 10X Genomics single cell ATAC-seq data, but I did not get any information in the cellSNP.base.vcf.gz file. Do you might know what the issue is? And whether do I need to set some specific parameters for scATAC-seq data?

Thanks in advance.

Best, Zhijun

hxj5 commented 2 years ago

Hi Zhijun,

Thank you for your feedback. Could you share your command line? I guess the issue may be caused by the improper setting of --UMItag for scATAC data.

Best Xianjie

zhijunyuu commented 2 years ago

Hi Xianjie,

Thanks so much for the quick reply. I tried to add the '--UMItag None' to my command line, it worked for my scATAC-seq data.

Cheers, Zhijun

Larrycpan commented 1 year ago

Hi Zhijun,

Thank you for your feedback. Could you share your command line? I guess the issue may be caused by the improper setting of --UMItag for scATAC data.

Best Xianjie

Thanks for the tool. I used the command cellsnp-lite -s possorted_bam.bam -b barcodes.tsv -O ./cellsnp_results -R genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf --minMAF 0.1 --minCOUNT 20 --UMItag None --genotype to call SNV from single-cell ATAC-seq data. There is no error during the running. However, most of the genotypes are valued -1. Are there any mistakes?

hxj5 commented 1 year ago

Hi, I don't know what genotype "-1" means, could you give one example?

Larrycpan commented 1 year ago

Hi, I don't know what genotype "-1" means, could you give one example?

It means that no SNP information is obtained for almost all sites, similar to NA. I've tried hg19 and hg38, but neither of them works.

hxj5 commented 1 year ago

could you share some SNPs in the output file cellSNP.cells.vcf.gz (just a few columns are fine, if you have many cells)? You may also want to look at issue #44 to double check whether the input barcodes are in the right format.