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has pileup-ed in total 0 SNPs #44
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Hi, is your data 10x scDNA-seq or scATAC-seq? If so, you may add |
It is 10x scDNA-seq! I'll add that option, Thanks! |
I am still getting all "0 SNPs" for the jobs even with minCOUNT down to 1. The command I used is: cellsnp-lite -s $BAM -b $BARCODE -O $OUT_DIR -p $PROC --minCOUNT 1 --countORPHAN --UMItag None If it helps the genome is Plasmodiophora brassicae (size: 24Mb/haploid) and I expect a few hundred cells with coverage between 0.1X and 1X. cellranger-dna (cnv) did not accept the reference but longranger (align) did and was used to make the input bam with processed barcodes (the 737K-crdna-v1.txt barcodes were placed in the longranger installation). |
Thanks for the details. Does the longranger bam file contain the tag for cell barcodes (the default value for |
Good point! The barcode tag name is BX with that pipeline. I ran with |
yes, suffixes (e.g., -1, -2, ...) should be added to the barcodes in the input list ( |
Just to let you know that this worked in the end with that last change. Thanks! |
I ran my dataset with two settings:
cellsnp-lite -s $BAM -b $BARCODE -O $OUT_DIR -p $PROC --minCOUNT 10
cellsnp-lite -s $BAM -b $BARCODE -O $OUT_DIR -p $PROC --minCOUNT 2 --countORPHAN
In both cases I get 0 SNP piled up.
This is the log so far for the test with countORPHAN above:
Any help is appreciated.
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