# \#hisat2

**URL:** https://help.galaxyproject.org/tag/hisat2/536.md

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## [Ouput unaligned reads into bam file with hisat2](https://help.galaxyproject.org/t/ouput-unaligned-reads-into-bam-file-with-hisat2/17587)

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**Author:** [@alixlem](https://help.galaxyproject.org/u/alixlem)\
**Replies:** 1\
**Last updated:** [March 18, 2026, 2:24pm UTC](https://help.galaxyproject.org/t/ouput-unaligned-reads-into-bam-file-with-hisat2/17587 "2026-03-18T14:24:49Z")

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Hello, I have a list of genes and a list of RNAs. For each gene, I would like to know how many RNAs do not align. I am using hisat2 for alignments, and it gives me a fastaqsanger file with the unaligned reads, but the b…

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## [HISAT2 Tool Failing: Guidance for known issue at UseGalaxy.org Feb 9 2026. README](https://help.galaxyproject.org/t/hisat2-tool-failing-guidance-for-known-issue-at-usegalaxy-org-feb-9-2026-readme/17436)

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**Author:** [@axao](https://help.galaxyproject.org/u/axao)\
**Replies:** 2\
**Last updated:** [February 10, 2026, 10:07pm UTC](https://help.galaxyproject.org/t/hisat2-tool-failing-guidance-for-known-issue-at-usegalaxy-org-feb-9-2026-readme/17436 "2026-02-10T22:07:08Z")

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I am trying to run HISAT2 for paired-end trimmed FASTQC datasets with the EBV reference genome, but all HISAT2 jobs fail immediately. The error message says, "/jetstream2/scratch/main/jobs/…/tool\_script.sh: line 10: hisa…

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## [HISAT2 reference genome for zooplankton](https://help.galaxyproject.org/t/hisat2-reference-genome-for-zooplankton/14187)

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**Author:** [@Justine\_Jay\_Santonin](https://help.galaxyproject.org/u/Justine_Jay_Santonin)\
**Replies:** 1\
**Last updated:** [December 16, 2024, 9:43pm UTC](https://help.galaxyproject.org/t/hisat2-reference-genome-for-zooplankton/14187 "2024-12-16T21:43:05Z")

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Hi, Good Day, is there a Reference genome for zooplankton like cytochrome c oxidase or CO1. Thank you and have a nice day

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## [HISAT2 Error--Input library collection must match # inputs for reference genome?](https://help.galaxyproject.org/t/hisat2-error-input-library-collection-must-match-inputs-for-reference-genome/13878)

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**Author:** [@brittb](https://help.galaxyproject.org/u/brittb)\
**Replies:** 2\
**Last updated:** [November 20, 2024, 7:05pm UTC](https://help.galaxyproject.org/t/hisat2-error-input-library-collection-must-match-inputs-for-reference-genome/13878 "2024-11-20T19:05:08Z")

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I downloaded some SRA accessions (which were downloaded as a collection; subsequent processing outputs from Trimmomatic are also in collections) using fasterq-dump, as well as a reference genome using NCBI Datasets Genom…

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## [HISAT2 output error](https://help.galaxyproject.org/t/hisat2-output-error/13688)

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**Author:** [@wcm](https://help.galaxyproject.org/u/wcm)\
**Replies:** 3\
**Last updated:** [October 21, 2024, 3:35am UTC](https://help.galaxyproject.org/t/hisat2-output-error/13688 "2024-10-21T03:35:38Z")

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Hi, I have recently been processing a large number of fastq files for RNA-seq analysis (150bp, paired-end, Illumina platform) following the tutorial below: (Hands-on: 1: RNA-Seq reads to counts / 1: RNA-Seq reads to co…