# \#custom-genome **URL:** https://help.galaxyproject.org/tag/custom-genome/52.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Reference genome for Drosophila issue](https://help.galaxyproject.org/t/reference-genome-for-drosophila-issue/18410)
**Author:** [@Maksym\_Dankovskyy](https://help.galaxyproject.org/u/Maksym_Dankovskyy)\ **Replies:** 7\ **Last updated:** [September 28, 2026, 5:41pm UTC](https://help.galaxyproject.org/t/reference-genome-for-drosophila-issue/18410 "2026-09-28T17:41:03Z")
Hello, I am trying to use RNA-STAR but I don’t believe the proper drosophila genome annotation is available under “built-in reference genome”. The two options are DM3 and release 6 ISO1 MT. However, I am looking specific… --- ## [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 … --- ## [BWA-MEM2 input file naming](https://help.galaxyproject.org/t/bwa-mem2-input-file-naming/17452)
**Author:** [@pbay653](https://help.galaxyproject.org/u/pbay653)\ **Replies:** 2\ **Last updated:** [February 13, 2026, 1:37am UTC](https://help.galaxyproject.org/t/bwa-mem2-input-file-naming/17452 "2026-02-13T01:37:40Z")
Firstly in order to get this to work I had to rename both fastqsanger files to exactly the same name, either R1/R2 or 1/2 or F/R did not work, after that it seems to work but I have other problems if someone can read the… --- ## [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 Custom Bowtie Tool Interface for Human Reference Genome Alignment](https://help.galaxyproject.org/t/request-for-custom-bowtie-tool-interface-for-human-reference-genome-alignment/17200)
**Author:** [@Armana](https://help.galaxyproject.org/u/Armana)\ **Replies:** 1\ **Last updated:** [January 6, 2026, 6:08pm UTC](https://help.galaxyproject.org/t/request-for-custom-bowtie-tool-interface-for-human-reference-genome-alignment/17200 "2026-01-06T18:08:14Z")
Hello Galaxy Team, I am working on small RNA-seq analysis using Galaxy, and I need to perform an alignment using the Bowtie tool with a human reference genome and my small RNA samples. I have already uploaded my sample … --- ## [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… --- ## [Newly launched BN rat genome assembly GRCr8 into the reference genome list?](https://help.galaxyproject.org/t/newly-launched-bn-rat-genome-assembly-grcr8-into-the-reference-genome-list/15778)
**Author:** [@daikez](https://help.galaxyproject.org/u/daikez)\ **Replies:** 1\ **Last updated:** [August 5, 2025, 6:51pm UTC](https://help.galaxyproject.org/t/newly-launched-bn-rat-genome-assembly-grcr8-into-the-reference-genome-list/15778 "2025-08-05T18:51:06Z")
Hi, may I ask a favor that if anyone could put the newly launched BN rat genome assembly GRCr8 (if possible also the other two assemblies? Rat UTH\_Rnor\_SHR\_Utx and Rat UTH\_Rnor\_WKY\_Bbb\_1.0?) into the Galaxy reference gen… --- ## [Adding a New Reference Genome for Cannabis sativa](https://help.galaxyproject.org/t/adding-a-new-reference-genome-for-cannabis-sativa/16055)
**Author:** [@a\_malik](https://help.galaxyproject.org/u/a_malik)\ **Replies:** 1\ **Last updated:** [July 29, 2025, 6:46am UTC](https://help.galaxyproject.org/t/adding-a-new-reference-genome-for-cannabis-sativa/16055 "2025-07-29T06:46:35Z")
Hi, I need to map RNA sequencing data against Cannabis sativa reference genome but its not present in the list. Could you please upload Cannabis sativa genome assembly " ASM2916894v1" and corresponding gene annotation f… --- ## [Mapping against a WGS reference](https://help.galaxyproject.org/t/mapping-against-a-wgs-reference/15830)
**Author:** [@richard64](https://help.galaxyproject.org/u/richard64)\ **Replies:** 2\ **Last updated:** [July 1, 2025, 11:02pm UTC](https://help.galaxyproject.org/t/mapping-against-a-wgs-reference/15830 "2025-07-01T23:02:18Z")
I want to map WGS against a reference but the species is not on the drop down reference list and it says I should contact Galaxy Team. Please advise --- ## [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… --- ## [Adding a reference genome to map RNAseq contig](https://help.galaxyproject.org/t/adding-a-reference-genome-to-map-rnaseq-contig/15240)
**Author:** [@LaurenceBindsch](https://help.galaxyproject.org/u/LaurenceBindsch)\ **Replies:** 1\ **Last updated:** [April 16, 2025, 10:14pm UTC](https://help.galaxyproject.org/t/adding-a-reference-genome-to-map-rnaseq-contig/15240 "2025-04-16T22:14:31Z")
Hello, I wish to MAP RNAseq contigs for transcriptomics analysis of a fungus Podosphaera xanthii, could you please add it to list of reference genomes? Thank you. --- ## [Reference genome for Camelus dromedarius](https://help.galaxyproject.org/t/reference-genome-for-camelus-dromedarius/15149)
**Author:** [@MYasir](https://help.galaxyproject.org/u/MYasir)\ **Replies:** 1\ **Last updated:** [April 3, 2025, 6:06pm UTC](https://help.galaxyproject.org/t/reference-genome-for-camelus-dromedarius/15149 "2025-04-03T18:06:43Z")
Hi Please add the reference genome for Camelus dromedarius in the app for Bowtie2. Thanks --- ## [Getting NCBI Reference genome indexed for tools: custom genome, reference genome, reference annotation](https://help.galaxyproject.org/t/getting-ncbi-reference-genome-indexed-for-tools-custom-genome-reference-genome-reference-annotation/14361)
**Author:** [@rkd](https://help.galaxyproject.org/u/rkd)\ **Replies:** 10\ **Last updated:** [March 14, 2025, 4:02pm UTC](https://help.galaxyproject.org/t/getting-ncbi-reference-genome-indexed-for-tools-custom-genome-reference-genome-reference-annotation/14361 "2025-03-14T16:02:29Z")
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file. The specified gene identifier attribute is ‘exon’ An example of attributes included in your GTF annotation is ‘ID=exon-XR\_… --- ## [Request to upload/add new version of reference genome of Aedes albopictus (Genome assembly AalbF5)](https://help.galaxyproject.org/t/request-to-upload-add-new-version-of-reference-genome-of-aedes-albopictus-genome-assembly-aalbf5/14774)
**Author:** [@NurulAdilah](https://help.galaxyproject.org/u/NurulAdilah)\ **Replies:** 1\ **Last updated:** [February 19, 2025, 1:05am UTC](https://help.galaxyproject.org/t/request-to-upload-add-new-version-of-reference-genome-of-aedes-albopictus-genome-assembly-aalbf5/14774 "2025-02-19T01:05:18Z")
Hi, I am currently analyzing my RNA-seq using Galaxy, and noticed the new version of Aedes albopictus reference genome is not available in the option. Could you please upload/add the latest reference genome of Aedes alb… --- ## [Custom reference genome annotation](https://help.galaxyproject.org/t/custom-reference-genome-annotation/5218)
**Author:** [@AlexaDean](https://help.galaxyproject.org/u/AlexaDean)\ **Replies:** 5\ **Last updated:** [February 14, 2025, 9:24pm UTC](https://help.galaxyproject.org/t/custom-reference-genome-annotation/5218 "2025-02-14T21:24:20Z")
Hello, I have the complete genome sequence (fasta format) from NCBI for my reference genome, but no access to any GTF/GFF3 file (it is a phage identified in our lab). I normalized the fasta file using NormalizeFasta. My… --- ## [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! --- ## [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… --- ## [RNA STAR options](https://help.galaxyproject.org/t/rna-star-options/14237)
**Author:** [@pooja\_harshan](https://help.galaxyproject.org/u/pooja_harshan)\ **Replies:** 1\ **Last updated:** [December 28, 2024, 8:52pm UTC](https://help.galaxyproject.org/t/rna-star-options/14237 "2024-12-28T20:52:01Z")
EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=51200000000is too small for your genome SOLUTION: please specify --limitGenomeGenerateRAM not less than 79547072778 and make that much RAM available Dec … --- ## [Addition Of Reference Genome](https://help.galaxyproject.org/t/addition-of-reference-genome/11692)
**Author:** [@pooja\_harshan](https://help.galaxyproject.org/u/pooja_harshan)\ **Replies:** 2\ **Last updated:** [December 23, 2024, 9:40am UTC](https://help.galaxyproject.org/t/addition-of-reference-genome/11692 "2024-12-23T09:40:47Z")
Could you please add Callorhinchus milii reference genome for RNASeq analysis? --- ## [RNAstar genome not available? Use a custom reference genome!](https://help.galaxyproject.org/t/rnastar-genome-not-available-use-a-custom-reference-genome/14062)
**Author:** [@drcottoncandy](https://help.galaxyproject.org/u/drcottoncandy)\ **Replies:** 1\ **Last updated:** [December 4, 2024, 6:32pm UTC](https://help.galaxyproject.org/t/rnastar-genome-not-available-use-a-custom-reference-genome/14062 "2024-12-04T18:32:02Z")
Hi Everyone, I am working with a very niche insect species and I am trying to perform RNAseq analysis using SRA files from NCBI. I have gotten to the point in the RNAseq training where I now have to map the RNAseq files… --- ## [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 … --- ## [NCBI BLAST+ blastx](https://help.galaxyproject.org/t/ncbi-blast-blastx/13650)
**Author:** [@saman\_ghodsi](https://help.galaxyproject.org/u/saman_ghodsi)\ **Replies:** 1\ **Last updated:** [October 10, 2024, 5:02pm UTC](https://help.galaxyproject.org/t/ncbi-blast-blastx/13650 "2024-10-10T17:02:34Z")
Hello, I have a 3-frame translated database of the planarian flatworm derived from its transcriptome. I want to exclude potential non-coding RNA that has been mistakenly translated in my database. I was considering perf… --- ## [reference genome for STARsolo](https://help.galaxyproject.org/t/reference-genome-for-starsolo/13627)
**Author:** [@Stephanie\_Dv](https://help.galaxyproject.org/u/Stephanie_Dv)\ **Replies:** 2\ **Last updated:** [October 9, 2024, 9:08am UTC](https://help.galaxyproject.org/t/reference-genome-for-starsolo/13627 "2024-10-09T09:08:40Z")
Dear, I would like to use STARsolo with this reference genome GCF\_000003025.6\_Sscrofa11.1 Would it be possible to include this as a reference genome (including annotation)? I see on the platform that it says “If your … --- ## [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 [Next page](https://help.galaxyproject.org/tag/custom-genome/52.md?match_all_tags=true&page=1&tags%5B%5D=custom-genome)