# \#custom-build **URL:** https://help.galaxyproject.org/tag/custom-build/285.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [A built-in reference genome is not available for zebrafish to utilise HISAT2](https://help.galaxyproject.org/t/a-built-in-reference-genome-is-not-available-for-zebrafish-to-utilise-hisat2/17651)
**Author:** [@Rahul\_Madaan](https://help.galaxyproject.org/u/Rahul_Madaan)\ **Replies:** 1\ **Last updated:** [April 13, 2026, 7:51pm UTC](https://help.galaxyproject.org/t/a-built-in-reference-genome-is-not-available-for-zebrafish-to-utilise-hisat2/17651 "2026-04-13T19:51:59Z")
How do i move ahead…Is there any built in reference genome available that I can just directly upload onto it (from ENSEMBL ?) --- ## [Add new version of reference genome: Tribolium castaneum (red flour beetle) Tcas5.2](https://help.galaxyproject.org/t/add-new-version-of-reference-genome-tribolium-castaneum-red-flour-beetle-tcas5-2/963)
**Author:** [@yoshitomoyasu](https://help.galaxyproject.org/u/yoshitomoyasu)\ **Replies:** 3\ **Last updated:** [April 7, 2026, 9:50pm UTC](https://help.galaxyproject.org/t/add-new-version-of-reference-genome-tribolium-castaneum-red-flour-beetle-tcas5-2/963 "2026-04-07T21:50:26Z")
Could you add the latest version of the Tribolium castaneum genome assembly (Tcas5.2) to the list? https://www.ncbi.nlm.nih.gov/genome?term=tribolium%20castaneum Thanks!! --- ## [Genome update sus scro: how to use a custom genome!](https://help.galaxyproject.org/t/genome-update-sus-scro-how-to-use-a-custom-genome/17466)
**Author:** [@Carolini](https://help.galaxyproject.org/u/Carolini)\ **Replies:** 2\ **Last updated:** [February 19, 2026, 10:48pm UTC](https://help.galaxyproject.org/t/genome-update-sus-scro-how-to-use-a-custom-genome/17466 "2026-02-19T22:48:20Z")
Dear Galaxy Team, I hope you are doing well. I am currently working with swine genomic data in Galaxy and noticed that the available reference genomes for Sus scrofa are limited to susScr2 and susScr3. However, for my … --- ## [How to view a result through IGV?](https://help.galaxyproject.org/t/how-to-view-a-result-through-igv/17106)
**Author:** [@abhi\_g](https://help.galaxyproject.org/u/abhi_g)\ **Replies:** 4\ **Last updated:** [January 7, 2026, 8:08am UTC](https://help.galaxyproject.org/t/how-to-view-a-result-through-igv/17106 "2026-01-07T08:08:43Z")
Hisat and Ivar and some other tool results are viewed through IGV automatically. I am not able to view it. Kindly guide to view results. Particularly for Ivar result, primer sequences. --- ## [Request for the add of genome](https://help.galaxyproject.org/t/request-for-the-add-of-genome/16561)
**Author:** [@yun\_he](https://help.galaxyproject.org/u/yun_he)\ **Replies:** 1\ **Last updated:** [December 10, 2025, 5:43pm UTC](https://help.galaxyproject.org/t/request-for-the-add-of-genome/16561 "2025-12-10T17:43:50Z")
Hello, Administrator. Could you please add the genome of this Aspergillus strain? Thank you.Aspergillus fumigatus A1163 genome assembly ASM15014v1 - NCBI - NLM --- ## [Is a "?" in featureCounts' database field a problem when using a non-built-in genome?](https://help.galaxyproject.org/t/is-a-in-featurecounts-database-field-a-problem-when-using-a-non-built-in-genome/16507)
**Author:** [@mmomeni](https://help.galaxyproject.org/u/mmomeni)\ **Replies:** 1\ **Last updated:** [November 24, 2025, 5:57pm UTC](https://help.galaxyproject.org/t/is-a-in-featurecounts-database-field-a-problem-when-using-a-non-built-in-genome/16507 "2025-11-24T17:57:27Z")
Hello and good day. I am teaching students using the Galaxy server tutorial “Reference-based RNA-Seq data analysis” . One of my students intends to analyze samples from the plant species Glycine max. Since the reference… --- ## [HISAT2 and RNA STAR reference genomes](https://help.galaxyproject.org/t/hisat2-and-rna-star-reference-genomes/15087)
**Author:** [@lterrazass](https://help.galaxyproject.org/u/lterrazass)\ **Replies:** 2\ **Last updated:** [April 25, 2025, 9:00pm UTC](https://help.galaxyproject.org/t/hisat2-and-rna-star-reference-genomes/15087 "2025-04-25T21:00:00Z")
I was trying to use Galaxy’s RNA-STAR and HISAT2 tools to create read count files for my RNA sequencing data, but there is no zebrafish (Danio rerio) reference genome available. I’m interested in the zebrafish genome and… --- ## [How to select a different reference genome from that already present using the tool RNA-STAR](https://help.galaxyproject.org/t/how-to-select-a-different-reference-genome-from-that-already-present-using-the-tool-rna-star/14681)
**Author:** [@Matteo\_Benda](https://help.galaxyproject.org/u/Matteo_Benda)\ **Replies:** 2\ **Last updated:** [February 10, 2025, 11:59pm UTC](https://help.galaxyproject.org/t/how-to-select-a-different-reference-genome-from-that-already-present-using-the-tool-rna-star/14681 "2025-02-10T23:59:30Z")
Hi everybody, i was asking how select a reference genome different to that already present in the option of RNA STAR. Thank you for your help! --- ## [Bowtie2 reference genome of Goat (Capra Hircus)](https://help.galaxyproject.org/t/bowtie2-reference-genome-of-goat-capra-hircus/13988)
**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")
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 … --- ## [Inquiry about lettuce genome](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608)
**Author:** [@Kelvin](https://help.galaxyproject.org/u/Kelvin)\ **Replies:** 2\ **Last updated:** [October 7, 2024, 5:20pm UTC](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608 "2024-10-07T17:20:58Z")
Hello, I want to ask if galaxy has lettuce reference genome. I’m considering using galaxy for my RNA-seq project in lettuce. Thank you --- ## [I am using HISAT2, but my reference genome Rickettsia rickettsii is missing in the dropdown list.](https://help.galaxyproject.org/t/i-am-using-hisat2-but-my-reference-genome-rickettsia-rickettsii-is-missing-in-the-dropdown-list/12948)
**Author:** [@Sonenshine](https://help.galaxyproject.org/u/Sonenshine)\ **Replies:** 13\ **Last updated:** [July 20, 2024, 11:59am UTC](https://help.galaxyproject.org/t/i-am-using-hisat2-but-my-reference-genome-rickettsia-rickettsii-is-missing-in-the-dropdown-list/12948 "2024-07-20T11:59:44Z")
Can someone in Galaxy add the genome for Rickettsia rickettsii to the dropdown list for HISAT2for the reads to --- ## [SICER is not available for the genome.](https://help.galaxyproject.org/t/sicer-is-not-available-for-the-genome/13218)
**Author:** [@moonmoondeb](https://help.galaxyproject.org/u/moonmoondeb)\ **Replies:** 1\ **Last updated:** [August 13, 2024, 6:59pm UTC](https://help.galaxyproject.org/t/sicer-is-not-available-for-the-genome/13218 "2024-08-13T18:59:17Z")
Hi I want to use the SICER tool for my histone chip-set analysis. But its showing “SICER is not available for the genome.” I am using Chicken genome assembly GRCg7b. (NCBI RefSeq assembly GCF\_016699485.2 and Submitted… --- ## [Bowtie2 brucella reference](https://help.galaxyproject.org/t/bowtie2-brucella-reference/13214)
**Author:** [@Harshita\_Mogaveera](https://help.galaxyproject.org/u/Harshita_Mogaveera)\ **Replies:** 1\ **Last updated:** [August 13, 2024, 6:28pm UTC](https://help.galaxyproject.org/t/bowtie2-brucella-reference/13214 "2024-08-13T18:28:56Z")
Hello, I want to align my WGS data with reference Brucella melitensis 16M. Please include brucella melitensis 16m in reference list --- ## [FreeBayes variant calling and Snpeff variant annotation](https://help.galaxyproject.org/t/freebayes-variant-calling-and-snpeff-variant-annotation/12406)
**Author:** [@Isa](https://help.galaxyproject.org/u/Isa)\ **Replies:** 18\ **Last updated:** [May 23, 2024, 9:26pm UTC](https://help.galaxyproject.org/t/freebayes-variant-calling-and-snpeff-variant-annotation/12406 "2024-05-23T21:26:27Z")
Hi, I am very new to Galaxy and bioinformatics overall (I have never had any education in it), however I am using Galaxy for my internship project, which involves analyzing NGS data from eight different yeast strains to… --- ## [How database assignments are used to access a fasta index: custom genomes, custom builds, server indexes](https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225)
**Author:** [@Choute](https://help.galaxyproject.org/u/Choute)\ **Replies:** 1\ **Last updated:** [April 17, 2024, 6:35pm UTC](https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225 "2024-04-17T18:35:32Z")
I’m currently encountering some issues while running a dataset through the Qualimap BamQC tool. Specifically, I’m receiving the following errors: Fatal error: Exit code 1 Input mapping file not found Has anyone experi… --- ## [hicBuildMatrix\_not\_working](https://help.galaxyproject.org/t/hicbuildmatrix-not-working/11904)
**Author:** [@Millicen](https://help.galaxyproject.org/u/Millicen)\ **Replies:** 1\ **Last updated:** [March 12, 2024, 9:22pm UTC](https://help.galaxyproject.org/t/hicbuildmatrix-not-working/11904 "2024-03-12T21:22:32Z")
hicBuildMatrix not working. I mapped my reads to a reference genome I uploaded to galaxy, using bowtie2. to obtain a .bam file. I want to run hicBuildMatrix but it is requesting for me to specify genome to be built. the… --- ## [Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at](https://help.galaxyproject.org/t/custom-genome-custom-build-how-to-use-a-genome-that-is-not-natively-indexed-at-the-server-you-are-working-at/10082)
**Author:** [@Fabiano\_Menegidio](https://help.galaxyproject.org/u/Fabiano_Menegidio)\ **Replies:** 3\ **Last updated:** [May 21, 2023, 10:39pm UTC](https://help.galaxyproject.org/t/custom-genome-custom-build-how-to-use-a-genome-that-is-not-natively-indexed-at-the-server-you-are-working-at/10082 "2023-05-21T22:39:43Z")
Reference data: no option available Contact the administrator of this Galaxy instance if you miss reference data (–config-dir) --- ## [Reference Genome](https://help.galaxyproject.org/t/reference-genome/11550)
**Author:** [@mycojon](https://help.galaxyproject.org/u/mycojon)\ **Replies:** 6\ **Last updated:** [January 24, 2024, 10:41pm UTC](https://help.galaxyproject.org/t/reference-genome/11550 "2024-01-24T22:41:28Z")
I have a question with bowtie2. When I search using a genome on the list, seems to be fine. But when using an .fna genome from ncbi or other, it gives me an error. Must be something I’m dojng wrong? --- ## [Bedgraph-to-bigwig error](https://help.galaxyproject.org/t/bedgraph-to-bigwig-error/11133)
**Author:** [@Adrian1](https://help.galaxyproject.org/u/Adrian1)\ **Replies:** 3\ **Last updated:** [November 14, 2023, 5:54pm UTC](https://help.galaxyproject.org/t/bedgraph-to-bigwig-error/11133 "2023-11-14T17:54:10Z")
tool: bedgraph-to-bigwig input: bedgraph files from MACS2 output problem: result bigwig file has 0 lines tool standard output: hashMustFindVal: ‘GL456210.1’ not found tool standard error" grep: write error: Broken pi… --- ## [Would it be possible for galaxy to include Camelus dromedarius reference genome in built in index ?](https://help.galaxyproject.org/t/would-it-be-possible-for-galaxy-to-include-camelus-dromedarius-reference-genome-in-built-in-index/10555)
**Author:** [@sagar\_khulape](https://help.galaxyproject.org/u/sagar_khulape)\ **Replies:** 4\ **Last updated:** [August 16, 2023, 3:38am UTC](https://help.galaxyproject.org/t/would-it-be-possible-for-galaxy-to-include-camelus-dromedarius-reference-genome-in-built-in-index/10555 "2023-08-16T03:38:35Z")
Would it be possible for galaxy to include Camelus dromedarius reference genome in built in index ? --- ## [RNA star with reference genome from history error](https://help.galaxyproject.org/t/rna-star-with-reference-genome-from-history-error/10570)
**Author:** [@Toyle1](https://help.galaxyproject.org/u/Toyle1)\ **Replies:** 1\ **Last updated:** [August 7, 2023, 4:58pm UTC](https://help.galaxyproject.org/t/rna-star-with-reference-genome-from-history-error/10570 "2023-08-07T16:58:15Z")
Hi, Apologies if I don’t manange to explain my problem very well I am quite new to analysising sequencing data. I have a new assembly and annotations in my galaxy account and wanted to align samples with RNA-star, then… --- ## [CHM13 T2T genome not found in options for some tools](https://help.galaxyproject.org/t/chm13-t2t-genome-not-found-in-options-for-some-tools/9947)
**Author:** [@TTP](https://help.galaxyproject.org/u/TTP)\ **Replies:** 8\ **Last updated:** [May 1, 2023, 5:41pm UTC](https://help.galaxyproject.org/t/chm13-t2t-genome-not-found-in-options-for-some-tools/9947 "2023-05-01T17:41:35Z")
Trying to use Wig/BedGraph-to-bigWig tool for a file generated with mapping to CHM13 T2T but the bedgraph file I am trying to convert does not allow me to designate the reference genome as CHM13 T2T (it does not come up … --- ## [Expanding the built-in reference genomes](https://help.galaxyproject.org/t/expanding-the-built-in-reference-genomes/10441)
**Author:** [@eghasemi](https://help.galaxyproject.org/u/eghasemi)\ **Replies:** 2\ **Last updated:** [July 12, 2023, 7:08pm UTC](https://help.galaxyproject.org/t/expanding-the-built-in-reference-genomes/10441 "2023-07-12T19:08:03Z")
Hi, I am a scientist working on Chlamydia infections. It would be very helpful for the Chlamydia community to add a few Chlamydiae reference genomes to Galaxy’s in-built reference genomes. Would you please let me know if… --- ## [missing reference genome (Aedes aegypti AaegL5.0)](https://help.galaxyproject.org/t/missing-reference-genome-aedes-aegypti-aaegl5-0/10202)
**Author:** [@Ouns87](https://help.galaxyproject.org/u/Ouns87)\ **Replies:** 5\ **Last updated:** [June 13, 2023, 8:09am UTC](https://help.galaxyproject.org/t/missing-reference-genome-aedes-aegypti-aaegl5-0/10202 "2023-06-13T08:09:06Z")
Hi, I am analysing the RNAseq data of the mosquitoe Aedes aegypti. I need to map my reads using the reference genome AaegL5.0\_GCA\_002204515.1. In the RNA STAR tab, there is no A.aegypti ref genome and it was mentioned … --- ## [Version and source of the galaxy built-in genome](https://help.galaxyproject.org/t/version-and-source-of-the-galaxy-built-in-genome/6471)
**Author:** [@Wenzhe\_Yin](https://help.galaxyproject.org/u/Wenzhe_Yin)\ **Replies:** 2\ **Last updated:** [May 5, 2023, 4:44pm UTC](https://help.galaxyproject.org/t/version-and-source-of-the-galaxy-built-in-genome/6471 "2023-05-05T16:44:20Z")
Hi, guys, I wonder where I can find the info of the version, the latest update time and source info of the built-in genomes. for instance, the Tair10 genome, is it the same with Ensemble Tair10 (05-Mar-2021) or the olde… --- ## [Source of built in reference genomes](https://help.galaxyproject.org/t/source-of-built-in-reference-genomes/10013)
**Author:** [@Akos](https://help.galaxyproject.org/u/Akos)\ **Replies:** 1\ **Last updated:** [May 5, 2023, 4:48pm UTC](https://help.galaxyproject.org/t/source-of-built-in-reference-genomes/10013 "2023-05-05T16:48:41Z")
Dear Galaxy Admins and Users, I would like to know the source of the Built-in genomes which can be found within the usegalaxy.eu website tools, i.e. RNA star. Is there a link / website /help-page that contains the vers… --- ## [Unresponsive page when load fasta file to build rice (Oryza sativa) genome](https://help.galaxyproject.org/t/unresponsive-page-when-load-fasta-file-to-build-rice-oryza-sativa-genome/9652)
**Author:** [@nzrf](https://help.galaxyproject.org/u/nzrf)\ **Replies:** 1\ **Last updated:** [April 13, 2023, 11:29pm UTC](https://help.galaxyproject.org/t/unresponsive-page-when-load-fasta-file-to-build-rice-oryza-sativa-genome/9652 "2023-04-13T23:29:14Z")
Hi Galaxy team, I would like to add rice genome as the reference genome to HISAT2, but when I load the fasta file, the page become unresponsive and snap notification appear. How can I solve this problem? Thanks. --- ## [Genome build for dog in RNA STAR](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603)
**Author:** [@Phil](https://help.galaxyproject.org/u/Phil)\ **Replies:** 5\ **Last updated:** [March 20, 2023, 10:27am UTC](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603 "2023-03-20T10:27:44Z")
I have noticed that many new reference genomes have appeared in RNA STAR. Would be great if Dog ((UU\_Cfam\_GSD\_1.0/canFam4) Mar.2020) could be added to this collection, then I can complete all my mappings with the same pi… --- ## [Adding new Reference genomes to the DeepVariant deep learning-based variant caller](https://help.galaxyproject.org/t/adding-new-reference-genomes-to-the-deepvariant-deep-learning-based-variant-caller/9347)
**Author:** [@player\_777](https://help.galaxyproject.org/u/player_777)\ **Replies:** 1\ **Last updated:** [January 26, 2023, 7:18pm UTC](https://help.galaxyproject.org/t/adding-new-reference-genomes-to-the-deepvariant-deep-learning-based-variant-caller/9347 "2023-01-26T19:18:23Z")
Please add new Reference genomes to the DeepVariant deep learning-based variant caller: Mycobacterium tuberculosis Pseudomonas aeruginosa Klebsiella pneumonia Acinetobacter baumannii E. coli Pneumococcus SARS-CoV-… --- ## [how to index the Tetrahymena genome?](https://help.galaxyproject.org/t/how-to-index-the-tetrahymena-genome/3250)
**Author:** [@asaettone](https://help.galaxyproject.org/u/asaettone)\ **Replies:** 3\ **Last updated:** [January 26, 2023, 7:22pm UTC](https://help.galaxyproject.org/t/how-to-index-the-tetrahymena-genome/3250 "2023-01-26T19:22:18Z")
The Tetrahymena thermophila isn’t indexed. Is this possible? It can be found at http://ciliate.org/index.php/home/downloads [Next page](https://help.galaxyproject.org/tag/custom-build/285.md?match_all_tags=true&page=1&tags%5B%5D=custom-build)