# \#bowtie2

**URL:** https://help.galaxyproject.org/tag/bowtie2/557.md

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## [Bowtie2 -- Paired end samples? Use a List of Pairs collection!](https://help.galaxyproject.org/t/bowtie2-paired-end-samples-use-a-list-of-pairs-collection/16341)

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**Author:** [@huiping](https://help.galaxyproject.org/u/huiping)\
**Replies:** 5\
**Last updated:** [October 3, 2025, 8:53pm UTC](https://help.galaxyproject.org/t/bowtie2-paired-end-samples-use-a-list-of-pairs-collection/16341 "2025-10-03T20:53:14Z")

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Dear Sir/Madam, Recently your Bowtie2 for paired-end reads analysis on Galaxy Europe platfrorm does not work. We wonder if you could fix it, thanks. Have a nice weekend. Best regards, Chen Huiping University Hospita…

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## [Reference genome from the history](https://help.galaxyproject.org/t/reference-genome-from-the-history/16262)

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**Author:** [@Oanh\_Ki\_u](https://help.galaxyproject.org/u/Oanh_Ki_u)\
**Replies:** 2\
**Last updated:** [September 22, 2025, 8:12pm UTC](https://help.galaxyproject.org/t/reference-genome-from-the-history/16262 "2025-09-22T20:12:58Z")

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Dear, I need to add the reference sequence of Vibrio proteolyticus strain to the galaxy reference genome sequence bank, please help me

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## [Bowtie2- Sort and Index](https://help.galaxyproject.org/t/bowtie2-sort-and-index/14684)

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**Author:** [@DHowell23](https://help.galaxyproject.org/u/DHowell23)\
**Replies:** 1\
**Last updated:** [February 8, 2025, 11:28am UTC](https://help.galaxyproject.org/t/bowtie2-sort-and-index/14684 "2025-02-08T11:28:27Z")

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Is the output bam file already sorted and indexed? If not, how can I index this file on galaxy? I cannot find the samtool index tool.

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## [Segmentation fault in featurecounts](https://help.galaxyproject.org/t/segmentation-fault-in-featurecounts/14476)

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**Author:** [@parvati.iyer](https://help.galaxyproject.org/u/parvati.iyer)\
**Replies:** 1\
**Last updated:** [January 17, 2025, 5:16pm UTC](https://help.galaxyproject.org/t/segmentation-fault-in-featurecounts/14476 "2025-01-17T17:16:30Z")

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Hello, I am facing issues with featurecounts, wherein I could not get any assigned features I realised that the RNAME of my bowtie file was slightly different than my reference gff3 file. Hence I edited the name in …

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## [Bowtie2 reference genome of Goat (Capra Hircus)](https://help.galaxyproject.org/t/bowtie2-reference-genome-of-goat-capra-hircus/13988)

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**Author:** [@Huseyin\_OZKAN](https://help.galaxyproject.org/u/Huseyin_OZKAN)\
**Replies:** 1\
**Last updated:** [November 25, 2024, 6:23pm UTC](https://help.galaxyproject.org/t/bowtie2-reference-genome-of-goat-capra-hircus/13988 "2024-11-25T18:23:03Z")

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Dear Friends, I have noticed that the reference genome for Capra hircus (Goat) is not available on usegalaxy. I have been advised to contact the Galaxy team regarding this matter. How can contact with the team? Thank …