cortes-ciriano-lab/SComatic

Using chromosome reference in Scomatic

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Arsamat commented

Hi,

I was running SComatic on single-cell data that I have. In the example, chr10 from grch38 was used as a reference. However, if I were to also see mutations in other chromosomes would I have to rerun step 4 separately for each chromosome with its respective grch38 reference? Thank you!

ArthurDondi commented

Hi, you could run it again from step 2 with the complete hg38.fa reference (available here https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) with --chrom all .

You can also run each chromosome separately, but from step 2, not step 4 (the BaseCellCounter file is already filtered).

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