Empty o/p matrix files

[Parul-Kudtarkar]

Hi @hxj5 We have scATAC-seq data from 3 pooled samples, the coverage is 980 raw read pairs per cell (shallow sequencing)

Mode 1a cellsnp-lite -b /home/ubuntu/outs/filtered_feature_bc_matrix/barcodes.tsv -s /home/ubuntu/outs/atac_possorted_bam.bam -R genome1K.phase3.SNP_AF5e4.chr1toX.hg38.vcf.gz -O cellsnp-PM_002 -p 20 --minMAF 0.1 --minCOUNT 20 --gzip

The output matrix files of cellSNP-lite are empty

%%MatrixMarket matrix coordinate integer general
%
0   3098    0

Please let me know what parameter combination would yield result. Thank you!

Best, Parul

[hxj5]

Hi Parul,

Thanks for the feedback. You may want to add --UMItag None option for scATAC data, as discussed in issue #26.

Best, Xianjie

[Parul-Kudtarkar]

Thanks @hxj5 that's helpful