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Merge branch 'master' of github.com:singleron-RD/sccite
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zhouyiqi91 committed Nov 22, 2024
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### Tag barcode

`tag_barcode_fasta` Path to the tag barcode fasta file. The read name in the fasta is the antibody ID and the sequence is the tag barcode. Example:
`tag_barcode_fasta` Path to the tag barcode fasta file. The read names in the fasta are the antibody ID and the sequences are the tag barcodes. Example:
```
>A0001_CD4
AACAAGACCCTTGAG
>A0002_CD8a
TACCCGTAATAGCGT
```

`r2_pattern` Specifies how to extract the index barcode sequence from the R2 read. Example: `L21C15` means the first 21 bases are the linker, the tag barcode starts at the 22nd base and is 15 bases long.
`r2_pattern` Specifies how to locate the tag barcode sequence in R2 reads. Example: `L21C15` means the first 21 bases are the linker, the tag barcode starts at the 22nd base and is 15 bases long.

### Running the pipeline with test data

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