Closed SaraVilla closed 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
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
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
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