diff --git a/jupyter-book/introduction/raw_data_processing.md b/jupyter-book/introduction/raw_data_processing.md index 1cc1b2d3..6ff51c0e 100644 --- a/jupyter-book/introduction/raw_data_processing.md +++ b/jupyter-book/introduction/raw_data_processing.md @@ -516,6 +516,17 @@ simpleaf index \ -t 8 ``` +````{admonition} Note on using an Apple silicon-based device +piscem is not available on conda for Apple silicon devices. To avoid errors during index building, add (`--no-piscem`): +simpleaf index \ +-o simpleaf_index \ +-f toy_human_ref/fasta/genome.fa \ +-g toy_human_ref/genes/genes.gtf \ +-r 90 \ +-t 8 \ +--no-piscem +```` + In the output directory `simpleaf_index`, the `ref` folder contains the _splici_ reference; The `index` folder contains the salmon index built upon the _splici_ reference. The next step, `simpleaf quant`, consumes an index directory and the mapping record FASTQ files to generate a gene count matrix. This command encapsulates all the major steps discussed in this section, including mapping, cell barcode correction, and UMI resolution.