# How to generate Nanopore fastq collection files for Unicycler?

**URL:** <https://help.galaxyproject.org/t/how-to-generate-nanopore-fastq-collection-files-for-unicycler/2662>\
**Category:** Uncategorized\
**Tags:** assembly, unicycler\
**Created:** [December 15, 2019, 3:05pm UTC](https://help.galaxyproject.org/t/how-to-generate-nanopore-fastq-collection-files-for-unicycler/2662 "2019-12-15T15:05:20Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![isrulik1](https://avatars.discourse-cdn.com/v4/letter/i/bb73d2/32.png) [@isrulik1](https://help.galaxyproject.org/u/isrulik1)\
**Post date:** [December 15, 2019, 3:05pm UTC](https://help.galaxyproject.org/t/how-to-generate-nanopore-fastq-collection-files-for-unicycler/2662/1 "2019-12-15T15:05:20Z")

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I was notice that collection files that were recognized by FastQC (for example) are not recognized by Unicycler.  
Thanks!  
Israel

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**Author:** ![mvdbeek](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mvdbeek/32/110_2.png) [@mvdbeek](https://help.galaxyproject.org/u/mvdbeek)\
**Post date:** [December 19, 2019, 5:37pm UTC](https://help.galaxyproject.org/t/how-to-generate-nanopore-fastq-collection-files-for-unicycler/2662/2 "2019-12-19T17:37:40Z")

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You’ll need to set the datatype to fastqsanger. This is usually auto-detected but fails for nanopore files which have unusual quality scores. You can set the datatype at upload or change it for existing datasets by clicking the pen icon on the dataset

![Screenshot 2019-12-19 at 18.35.46](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/6/6fbaffa4a606ff37f235116f64a55f65e5194852.png)

then click on the datatype tab and select fastqsanger or fastqsanger.gz depending on whether your data is compressed or not:

 ![Screenshot 2019-12-19 at 18.35.53](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/5/54869126e5416628a4669aaae38dae38609ef482.png)

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**Author:** ![isrulik1](https://avatars.discourse-cdn.com/v4/letter/i/bb73d2/32.png) [@isrulik1](https://help.galaxyproject.org/u/isrulik1)\
**Post date:** [December 20, 2019, 12:08pm UTC](https://help.galaxyproject.org/t/how-to-generate-nanopore-fastq-collection-files-for-unicycler/2662/3 "2019-12-20T12:08:11Z")

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Dear Marius,  
Many thanks for the explanations!  
Merry Christmas and Happy New Year,  
Israel