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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

mouse SNPs recommendation #15

Closed SaraVilla closed 2 years ago

SaraVilla commented 2 years ago

Hi. I would like to use scSplit in my mouse 10X sequencing, is there any SNP list that you can recommend for mouse samples? Many thanks, Sara

jon-xu commented 2 years ago

Hi Sara,

We didn't test any common variants for mouse, maybe you can try this one: https://www.sanger.ac.uk/data/mouse-genomes-project/

However, the common variant is optional, so you don't have to use it.

Cheers, Jon

SaraVilla commented 2 years ago

Hi Jon,

wonderful, many thanks for this. I'm just finishing the QC and preprocessing of the bam and I was also wondering what would be the fata reference sequence required to run freebayes? The mouse genome in fasta format? Trying to get it from https://hpc.nih.gov/apps/db.php?g=Mouse, but would appreciate any advice. Thanks again! Sara

jon-xu commented 2 years ago

Sara, You can find detail explanations of freebayes on their website: https://github.com/freebayes/freebayes Yes you need mouse reference genome in FASTA format. Jon