# Assistance with Filtlong Tool for Quality Filtering of FastQ Data

**URL:** <https://help.galaxyproject.org/t/assistance-with-filtlong-tool-for-quality-filtering-of-fastq-data/11141>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting, fastqsanger\
**Created:** [November 14, 2023, 3:42pm UTC](https://help.galaxyproject.org/t/assistance-with-filtlong-tool-for-quality-filtering-of-fastq-data/11141 "2023-11-14T15:42:01Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [November 14, 2023, 6:04pm UTC](https://help.galaxyproject.org/t/assistance-with-filtlong-tool-for-quality-filtering-of-fastq-data/11141/2 "2023-11-14T18:04:09Z")

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> [@ge96dah](#):
>
> I’ve chosen Filtlong for filtering as my output data files are in .fastq or .fastq.gz format, and unfortunately, they are not in fastqsanger or similar formats compatible with other filtering tools.

Hi @ge96dah

What format are your data in? What does FastQC report a the top of the report for the quality score scaling?

You could also try using the auto-detect datatype function [Detecting the datatype (file format)](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_detect_datatype.html). Maybe the quality score scaling is already Fastq Sanger. The Upload tool would also detect the datatype (try using all defaults during Upload, especially for read data). If Galaxy guesses wrong, that is usually an important clue about some format/content problem.

I’m also wondering how the data was input to the tool. “Dragging and Dropping” is never recommended. The format requirements are expecting .fastqsanger.

Most fastq data uses that same quality scale scoring now, even long reads.

 ![fitlong-usage](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/0/08f99193c3962b9c468d98da339a87d477527964.png)

Related Q&A [fastq unavailable -- Tool does not recognize inputs? How to check why - #2 by jennaj](https://help.galaxyproject.org/t/fastq-unavailable-tool-does-not-recognize-inputs-how-to-check-why/8925/2)

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