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Update README.md
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alihamraoui authored Sep 3, 2024
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Expand Up @@ -104,15 +104,6 @@ The human GRCh38 [reference transcriptome](https://ftp.ensembl.org/pub/release-1
--gtf dataset/genes.gtf
```

##### USING SPARSIM PRESET MATRICES (e.g Chu et al. 10X Genomics datasets)

```bash
nextflow run main.nf --matrix Chu_param_preset \
--transcriptome datasets/Homo_sapiens.GRCh38.cdna.all.fa \
--features gene_name \
--gtf datasets/Homo_sapiens.GRCh38.112.gtf
```

##### WITH PCR AMPLIFICTION

```bash
Expand All @@ -136,6 +127,15 @@ nextflow run main.nf --matrix Chu_param_preset \
--cell_types_annotation dataset/sub_pbmc_cell_type.csv
```

##### USING A SPARSIM PRESET MATRIX (e.g Chu et al. 10X Genomics datasets)

```bash
nextflow run main.nf --matrix Chu_param_preset \
--transcriptome datasets/Homo_sapiens.GRCh38.cdna.all.fa \
--features gene_name \
--gtf datasets/Homo_sapiens.GRCh38.112.gtf
```

##### WITH PERSONALIZED ERROR MODEL

```bash
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