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I have three suggestions/questions about cellSNP and cellsnp-lite:
Would you consider using the "start" and "stop" parameters in pysam.pileup to allow users to achieve faster SNP detection within a region/gene of interest?
One of my gene of interest is known to be frequently disrupted by frameshift mutations / indels, but cellSNP only support single-nucleotide variant detection. Could the pipeline be modified to consider indels?
Is it possible to input two or multiple scRNA-seq samples and identify sites that are different across samples?
Thank you!
Best regards,
Yiyun
The text was updated successfully, but these errors were encountered:
ychenab
changed the title
Adapting cellSNPs for gene-of-interest / indels / multiple scRNA-seq samples
Adapting cellSNP for gene-of-interest / indels / multiple scRNA-seq samples
Jun 20, 2023
Hi Yuanhua,
I have three suggestions/questions about cellSNP and cellsnp-lite:
Would you consider using the "start" and "stop" parameters in pysam.pileup to allow users to achieve faster SNP detection within a region/gene of interest?
One of my gene of interest is known to be frequently disrupted by frameshift mutations / indels, but cellSNP only support single-nucleotide variant detection. Could the pipeline be modified to consider indels?
Is it possible to input two or multiple scRNA-seq samples and identify sites that are different across samples?
Thank you!
Best regards,
Yiyun
The text was updated successfully, but these errors were encountered: