# :icon-sort-desc: Sort linked-read data by barcode

Sometimes you want/need linked-read data to be sorted by barcode.
In order to accomplish this with Djinn, the barcode **must** be in a SAM tag (e.g. `BX`, `BC`) FASTQ or SAM/BAM format. If your 
barcodes aren't in a SAM tag, consider using [!badge corners="pill" text="fastq convert"](/convert.md) or
[!badge corners="pill" text="standardize"](/standardize.md) to convert it into a compliant format.

## FASTQ

```bash usage
djinn fastq sort SAMTAG PREFIX INPUT...
```

```bash example | sort fastq with barcodes in BC tag
djinn fastq sort BC pebbles_sorted data/pebbles.R1.fq.gz data/pebbles.R2.fq.gz
```

### :icon-terminal: Running Options
{.compact}
| argument          | description                                                                   |
|:------------------|:------------------------------------------------------------------------------|
| `SAMTAG`          | [!badge variant="info" text="required"] 2-letter name of the SAM tag storing the barcode (e.g. `BC` or `BX`)  |
| `PREFIX`          | [!badge variant="info" text="required"] output filename prefix                |
| `INPUT`          | [!badge variant="info" text="required"] FASTQ file or file pair         |
| `-t` `--threads`  | Number of threads to use (default: 4)                                                  |

## SAM

```bash usage
djinn sam sort SAMTAG INPUT
```

```bash example | sort fastq with barcodes in BC tag
djinn sam sort BC data/pebbles.bam
```

### :icon-terminal: Running Options
{.compact}
| argument          | description                                                                   |
|:------------------|:------------------------------------------------------------------------------|
| `SAMTAG`          | [!badge variant="info" text="required"] 2-letter name of the SAM tag storing the barcode (e.g. `BC` or `BX`)  |
| `INPUT`          | [!badge variant="info" text="required"] SAM/BAM file         |
| `-t` `--threads`  | Number of threads to use (default: 4)                                                  |