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jon-xu / scSplit

Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.
MIT License
39 stars 9 forks source link

Running time #26

Closed IBDgenomics closed 6 months ago

IBDgenomics commented 10 months ago

Hi,

Running scSplit count is taking forever. I assume is because the number of variants from freebayes is pretty high (>1.3M). I'm running a pool of 4 samples, ~11k cells.

Num Pos: 312637, Num barcodes: 11037

Do you have any recommendation on how to handle this? Filtering somehow the freebayes vcf to reduce the number of variants? Would it make sense to run scSplit count by region/chromosome and build a consensus after that?

Thanks in advance

jon-xu commented 10 months ago

Hi,

1.3 Million looks a bit too many for me. And this should be the reason of long running time.

Cheers,

Jon

On 10 Nov 2023, at 19:47, IBDgenomics @.***> wrote:



Hi,

Running scSplit count is taking forever. I assume is because the number of variants from freebayes is pretty high (>1.3M). I'm running a pool of 4 samples, ~11k cells.

Do you have any recommendation on how to handle this? Filtering somehow the freebayes vcf to reduce the number of variants? Would it make sense to run scSplit count by region/chromosome and build a consensus after that?

Thanks in advance

— Reply to this email directly, view it on GitHubhttps://github.com/jon-xu/scSplit/issues/26, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AJXMHDCKZHFQEWNHFMFHDZTYDXZ3BAVCNFSM6AAAAAA7F44INCVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE4DOMRYGE2TSOI. You are receiving this because you are subscribed to this thread.Message ID: @.***>