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Update raw_data_processing.md
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avoid missing piscem path during index generation
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zimea authored Feb 8, 2024
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Expand Up @@ -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.
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