---
title: What file formats can I use for secondary analysis?
description: Learn the expected format and names of .fastq files used for our secondary analyses worksets.
---

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# What file formats can I use for secondary analysis?

## Learn the expected format and names of .fastq files used for our secondary analyses worksets.

The format of the raw .fastq files to be uploaded for each sample depends on the sequencing platform used. File names must conform to each sequencer's file naming convention. Files need to be compressed, using the .gz (gzip) extension, before they can be imported into the platform.

In the case of paired-end sequencing, two files are expected, corresponding to reads from both ends of each molecule. Paired-end files are automatically combined into a single sample.

When a sample has been correctly detected by the platform at the time of import, the full name of the file is displayed. It is then possible to rename the file by clicking on it.

The following sequencers are supported by the platform:

- Illumina : fastq.gz format, paired-end only
- Element Biosciences : fastq.gz format, paired-end only
- MGI : format fastq.gz, paired-end only. The expected file names are indicated below: 
    - **either**: sample\_1.fq.gz **and** sample\_2.fq.gz
    - **or:** flowcellID\_L01\_sample\_1.fq.gz **and** flowcellID\_L01\_sample\_2.fq.gz

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