> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003376.md).

# How to download only FASTQs from a BaseSpace project using BaseSpace CLI

The BaseSpace CLI download command coupled with the `--extension fastq.gz` option will download all **FASTQs** stored in the specified **Project**:

```
bs download project -i &lt;ProjectID&gt; -o &lt;Destination&gt; --extension fastq.gz  
```

To download a subset of specific files such as a subset of FASTQ files from a BaseSpace project it is possible to use the `contents` command to list all files, then filter them as desired before downloading. Here is an example way to download all Lane 1 FASTQ files of sample names ending with "Rep1" to the current directory.

Windows:

```
bs contents project -i &lt;ProjectID&gt; -f csv > files-in-project.csv  
findstr /R "Rep1_.*L001.*fastq.gz" files-in-project.csv > filtered-fastqfiles-in-project.csv  
for /f "tokens=1 delims=," %a in (filtered-fastqfiles-in-project.csv) do bs download file -i %a -o . --no-metadata  
```

Unix/Mac:

```
bs contents project -i &lt;ProjectID&gt; -f csv > files-in-project.csv  
grep 'Rep1_.*L001.*fastq.gz' files-in-project.csv > filtered-fastqfiles-in-project.csv  
while IFS=',' read -r first_value rest; do bs download file -i "$first_value" -o . --no-metadata; done < filtered-fastqfiles-in-project.csv  
```

It is possible to filter results directly using `contents` command with combination of exclude and include options

```
bs contents project -i 395620236 -f csv --exclude=* --include=*Rep1_*L001*.fastq.gz > filtered-fastqfiles-in-project.csv  
```

For further information, see [CLI examples](https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-examples#Downloadfilesassociatedwithaproject) page.\
For more information on listing entities, see [How to list BaseSpace entities using BaseSpace CLI](https://github.com/illumina-swi/illumina-knowledge/tree/master/docs/Software/Cloud-Software/Reference_Material/000003682.md)\
For uploading FASTQ or downloading FASTQ files from an input run folder, see [How to upload and download FASTQ files to BaseSpace with BaseSpace CLI](/software/basespace-cli/software-basespace-cli-reference_material-list/000001138.md)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #3376), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003376%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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