Hi, I have single-cell whole-genome sequencing data for four stages of erythrocyte differentiation, with each stage having two replicates (n=2). How can I use Sarek to save the aligned and unaligned reads, and how can I find the differences between each stage? TIA

nf-core/sarek is not designed for single-cell data. It doesn't know how to distinguish cell by their barcode and analyze each one separately. As far as I know, the tools it uses also are not optimized in any way for the lower read depths and potentially missing site I would expect in single cell data. You can of course treat the single cell data like regular whole-tissue samples if you can either get the trimmer to remove all single-cell-specific adapters or do that yourself before running the pipeline, but you won't get any single-cell resolution and the results may be hard to interpret, depending on the source of your data. The aligned CRAMs (or BAMs, if desired) can be retained with the `--save_mapped` parameter. If by "unaligned" you mean trimmed, those are either the input for the pipeline, or if you can get the

fastp

in the pipeline to work for you (with

--trim_fastq

), you can specify

--save_trimmed

.