# \#fastq-format **URL:** https://help.galaxyproject.org/tag/fastq-format/472.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [FastQ ASCII table for raw sequences' QC](https://help.galaxyproject.org/t/fastq-ascii-table-for-raw-sequences-qc/15892)
**Author:** [@lcfiorini](https://help.galaxyproject.org/u/lcfiorini)\ **Replies:** 2\ **Last updated:** [July 4, 2025, 8:41am UTC](https://help.galaxyproject.org/t/fastq-ascii-table-for-raw-sequences-qc/15892 "2025-07-04T08:41:19Z")
Hello everybody, I’ve been reading many tutorials and educational materials about basic .fastq files quality control procedures but I’m confused because it doesn’t seem to apply to my experimental data. I was able to up… --- ## [BAM file from HISAT2 to fastq for Genome assembly](https://help.galaxyproject.org/t/bam-file-from-hisat2-to-fastq-for-genome-assembly/15031)
**Author:** [@John\_Kim](https://help.galaxyproject.org/u/John_Kim)\ **Replies:** 3\ **Last updated:** [March 18, 2025, 6:40pm UTC](https://help.galaxyproject.org/t/bam-file-from-hisat2-to-fastq-for-genome-assembly/15031 "2025-03-18T18:40:56Z")
Hi friends!, I would like to ask if you know of any tools to convert BAM alignment files (which I generated in Galaxy using HISAT2) into FASTQ files, suitable for genome assembly. I used bedtools bamtofastq, but I recei… --- ## [Breseq fastq format troubleshooting](https://help.galaxyproject.org/t/breseq-fastq-format-troubleshooting/14670)
**Author:** [@davide\_bersanetti](https://help.galaxyproject.org/u/davide_bersanetti)\ **Replies:** 3\ **Last updated:** [February 8, 2025, 11:19am UTC](https://help.galaxyproject.org/t/breseq-fastq-format-troubleshooting/14670 "2025-02-08T11:19:42Z")
Hi everyone I am trying to run Breseq but I keep getting the error shown in the image, no matter what type of data I use ( raw reads, trimmed, assemblies) What could be the reason? Thank you for any kind of help --- ## [UCSC Reference Genome and GTF Fatal Error no valid exons in the GTF file](https://help.galaxyproject.org/t/ucsc-reference-genome-and-gtf-fatal-error-no-valid-exons-in-the-gtf-file/14367)
**Author:** [@drcottoncandy](https://help.galaxyproject.org/u/drcottoncandy)\ **Replies:** 3\ **Last updated:** [January 22, 2025, 7:41pm UTC](https://help.galaxyproject.org/t/ucsc-reference-genome-and-gtf-fatal-error-no-valid-exons-in-the-gtf-file/14367 "2025-01-22T19:41:32Z")
Good morning! I am performing RNAstar and feature counts on the species camponotus floridanus. I have followed the tutorial training for RNAseq analysis of d.mel provided by Galaxy, and I had no issues. In this tutorial… --- ## [Faster Download and Extract Reads in FASTQ and ENA reads are slightly different](https://help.galaxyproject.org/t/faster-download-and-extract-reads-in-fastq-and-ena-reads-are-slightly-different/13118)
**Author:** [@rand.zoabi](https://help.galaxyproject.org/u/rand.zoabi)\ **Replies:** 2\ **Last updated:** [September 27, 2024, 9:10pm UTC](https://help.galaxyproject.org/t/faster-download-and-extract-reads-in-fastq-and-ena-reads-are-slightly-different/13118 "2024-09-27T21:10:09Z")
Hi all, I just noticed there is a slight difference between FASTQ files downloaded using the ‘ Faster Download and Extract Reads in FASTQ’ tool and the one published on ENA for the same accession, does anybody know why … --- ## [How to upload .fastq?](https://help.galaxyproject.org/t/how-to-upload-fastq/9280)
**Author:** [@Sofi](https://help.galaxyproject.org/u/Sofi)\ **Replies:** 3\ **Last updated:** [January 11, 2023, 10:41pm UTC](https://help.galaxyproject.org/t/how-to-upload-fastq/9280 "2023-01-11T22:41:00Z")
Hello! I am very new to galaxy and it is my first problem :frowning: I have gz archive with .fastq, but when it unpacking it still .fastq (not .fastq.gz) And when I upload my file it appears to the right and it is red.… --- ## [Trim Galore error due to problematic fastq format](https://help.galaxyproject.org/t/trim-galore-error-due-to-problematic-fastq-format/1253)
**Author:** [@shamjdeed](https://help.galaxyproject.org/u/shamjdeed)\ **Replies:** 7\ **Last updated:** [November 26, 2019, 7:34am UTC](https://help.galaxyproject.org/t/trim-galore-error-due-to-problematic-fastq-format/1253 "2019-11-26T07:34:26Z")
Hello, Please I have a question regarding ChIP-Seq data analysis using Galaxy platform! During the trimming step (using Trim Galore) for ChIP-Seq data, I got error message: Fatal error: Exit code 1 () Path to Cutadapt … --- ## [HISAT2 - Could not display BAM file](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303)
**Author:** [@artem](https://help.galaxyproject.org/u/artem)\ **Replies:** 6\ **Last updated:** [October 24, 2019, 12:09am UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303 "2019-10-24T00:09:03Z")
Hello! I have local Galaxy installed. Also I used Data Manager for creating indexes. Galaxy - 19.05 HISAT2 - 2.1.0+galaxy5 I have just tried to run Hisat2 on usegalaxy.org with one of my files and it run successfully… --- ## [bowtie2 fatal error message](https://help.galaxyproject.org/t/bowtie2-fatal-error-message/2091)
**Author:** [@Michel](https://help.galaxyproject.org/u/Michel)\ **Replies:** 4\ **Last updated:** [September 12, 2019, 6:38pm UTC](https://help.galaxyproject.org/t/bowtie2-fatal-error-message/2091 "2019-09-12T18:38:32Z")
Good morning, I am running a ChIP-Seq (pair-end) analysis for the first time and managed to find a good pipeline to follow. The pipeline is described in the following way FASTQC - TRIMMOMATIC - FASTQC - BOWTIE2 - MACS2… --- ## [Should or can paired-end fastq be converted to single-end fastq -- and the reverse?](https://help.galaxyproject.org/t/should-or-can-paired-end-fastq-be-converted-to-single-end-fastq-and-the-reverse/1648)
**Author:** [@amir](https://help.galaxyproject.org/u/amir)\ **Replies:** 5\ **Last updated:** [July 3, 2019, 7:59am UTC](https://help.galaxyproject.org/t/should-or-can-paired-end-fastq-be-converted-to-single-end-fastq-and-the-reverse/1648 "2019-07-03T07:59:45Z")
how can i turn a single end data, into the paired end data and opposite( paired end into single end data) ?