# :icon-git-compare: Convert between FASTQ formats

In the event you need your linked-read data converted into a different linked-read format, djinn has you covered.
We might disagree on the fragmented format landscape, but that doesn't mean you
shouldn't be able to use your data how and where you want to. This command converts a paired-end read set of FASTQ
files between the common linked-read FASTQ types.

```bash usage
djinn fastq convert PREFIX TARGET FQ1 FQ2
```

```bash example | tellseq → stlfr
djinn fastq convert data/orcs_stlfr stlfr data/orcs.R1.fq.gz data/orcs.R2.fq.gz
```

Auto-detects the input format as one of 10X, haplotagging, TELLseq, or stLFR,
and converts it to the format provided as the `TARGET` positional argument. If the
input data is in 10X format, where the barcode is the first [usually] 16 bases in the R1 sequence,
you will need to provide a `--barcodes` file that lets Djinn know what barcodes to look for.
In all cases, a file will be created with the barcode conversion map.

==- example `--barcodes` file
```
ATGGAAGCCGTAGTTA
ACGGAAGCCGTAGTTC
ATGGAAGAAATAGTTA
ATGTTTGCCGTAGTTT
```
===

## :icon-move-to-end: Conversion targets

{.compact}
| `TARGET`       | barcode format                                     | example                     |
|:---------------|:---------------------------------------------------|:----------------------------|
| `10x`          | the first N base pairs of R1, given `--barcodes`   |                             |
| `haplotagging` | a `BX:Z:ACBD` SAM tag in the sequence header       | `@SEQID BX:Z:A01C93B56D11`  |
| `stlfr`        | `#1_2_3` format appended to the sequence ID        | `@SEQID#1_2_3`              |
| `tellseq`      | `:ATCG` format appended to the sequence ID         | `@SEQID:GGCAAATATCGAGAAGTC` |

## :icon-terminal: Running Options
{.compact}
| argument          | description                                                                   |
|:------------------|:------------------------------------------------------------------------------|
| `PREFIX`          | [!badge variant="info" text="required"] output filename prefix                |
| `TARGET`          | [!badge variant="info" text="required"] target format for output FASTQ files  |
| `FQ1`             | [!badge variant="info" text="required"] forward reads of FASTQ pair           |
| `FQ2`             | [!badge variant="info" text="required"] reverse reads of FASTQ pair           |
| `-b` `--barcodes` | [!badge variant="info" text="conditional"] file of nucleotide barcodes (one per line) to identify inline barcodes in input 10X data  |
| `-c` `--cache-size` |[!badge variant="ghost" text="hidden"] number of reads to store before writing (bigger is faster, default: `10000`) |
| `-t` `--threads`    | Number of threads to use for writing compressed output fastq files (default: 2)                                                                              |