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Update docs/usage.md
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Co-authored-by: Gregor Sturm <[email protected]>
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heylf and grst authored Dec 3, 2023
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Expand Up @@ -123,11 +123,13 @@ If you are using cellranger-arc you have to add the column _sample_type_ (atac f
An example samplesheet for a dataset called test_scARC that has two sequencing runs for the scATAC and one seqeuncing run
from two lanes for the scRNA could look like this:

```csv
sample,fastq_1,fastq_2,fastq_barcode,sample_type
test_scARC,path/test_scARC_atac_rep1_S1_L001_R1_001.fastq.gz,path/test_scARC_atac_rep1_S1_L001_R2_001.fastq.gz,path/test_scARC_atac_rep1_S1_L001_I2_001.fastq.gz,atac
test_scARC,path/test_scARC_atac_rep2_S2_L001_R1_001.fastq.gz,path/test_scARC_atac_rep2_S2_L001_R2_001.fastq.gz,path/test_scARC_atac_rep2_S2_L001_I2_001.fastq.gz,atac
test_scARC,path/test_scARC_gex_S1_L001_R1_001.fastq.gz,path/test_scARC_gex_S1_L001_R2_001.fastq.gz,,gex
test_scARC,path/test_scARC_gex_S1_L002_R1_001.fastq.gz,path/test_scARC_gex_S1_L002_R2_001.fastq.gz,,gex
```

#### Config file and index

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