# BAM index, fasta indexes, display applications, custom genome builds, IGV **URL:** \ **Category:** Resources\ **Tags:** igv, resources\ **Created:** [September 22, 2025, 7:10am UTC](https://help.galaxyproject.org/t/bam-index-fasta-indexes-display-applications-custom-genome-builds-igv/16283 "2025-09-22T07:10:07Z")\ **Posts on this page:** 1\ **Showing post:** 4
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 22, 2025, 7:13pm UTC](https://help.galaxyproject.org/t/bam-index-fasta-indexes-display-applications-custom-genome-builds-igv/16283/4 "2025-09-22T19:13:59Z")
HI @Prabhsimran_Singh If you already mapped with Bowtie in Galaxy, then @igor advice applies. > [@igor](#): > > If you map reads (create a bam file) in Galaxy, bam.bai index file will be created automatically. The `output.bam` will be in your history as a dataset. The `output.bam.bai` index is not directly displayed as a seperate dataset, but it is part of this compound dataset. You can download both files [using the disc icon](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_icons.html) if you want to use this data outside of Galaxy. They already exist. Click on that disc icon – you’ll see the choice for both files. Download them separately to get both. _Screenshot of a bam dataset with the disc icon activated_ * * * ## ![bam-disc-icon](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/b/b82049298b36a648b5976cc39988c0d4aac23df8.png) **Now, you also have more choices!** ### 📄 Single file hosting for display applications _WITHOUT genomic fasta indexes_ To view just that single bam output in IGV, you can click on the visualize icon to access display applications. This still uses Galaxy as the data host, but when there is no database assignment, a single on-demand _generic fasta_ index will be created for transfer over to display applications. WARNINGS: 1. There will be no genomic DNA sequence reference included because there is no fasta/fasta.fai index attached to the dataset! 2. Additional files **cannot be loaded** into the same display. * * * ## ![bam-visualize-icon-WITHOUT-database-assigned](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/5/5c70a79d1e98c1432b17efbc1123daf0a499a133.png) ### 📄 📄 📄 Multiple file hosting for display applications _WITH genomic fasta indexes_ To view multiple datasets all together in a display application, you can also click on the visualize icon to access display applications. This uses Galaxy as the data host, and when there is a database assignment, this attaches your genome’s _specific fasta_ index for transfer over to display applications. BENIFITS: 1. Genome DNA backbone included in the display. 2. Any dataset sharing the same database assignment can be loaded into the same display. 3. Native database keys can be assigned and Custom database dbkeys can be created and assigned. Both will work the same! Not sure how to create and assign a Custom database? - [https://training.galaxyproject.org/training-material/faqs/galaxy/reference\_genomes\_custom\_genomes.html](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html) - With many examples at this forum, see #custom-genome #custom-build * * * ## ![bam-visualize-icon-WITH-database-assigned](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/6/6b020170d47c75e26dd1e42fa6f688b4d752bbec.png) 🚀 What to do? Since you have a genome fasta file already, creating a custom database build key, then assigning it to your datasets seems like a good choice! This will allow you to load all of the data into a local IGV application and view everything together. Now, with IGV, you will also need to _set up your custom genome_! If you already have IGV set up with your custom genome, just make sure to label your custom genome in Galaxy the same way. **The database “dbkey” label must be the same everywhere to instruct the applications to use the same fasta index.** Avoid mixing up assemblies here or expect problems with the data coordinates. This topic has more details, some that overlap with what is already above, but maybe it provides some more context? 🙂 > [@Opening Unicycler assemblies with IGV local](https://help.galaxyproject.org/t/opening-unicycler-assemblies-with-igv-local/2653/4): > > IGV is a different application. The methods to create a “New Genome” in your own IGV are below. The preparations steps will require that you index the fasta with samtools as part of that process. Or you can create the fasta index in Galaxy and download that along with the fasta. > > - IGV: [IGV Desktop Application](https://software.broadinstitute.org/software/igv/LoadGenome) ### Connecting it all together 1. IGV configured with your custom genome 2. Galaxy configured with your custom genome 3. the custom database dbkey (fasta index) assigned to datasets in Galaxy 4. then when the **database dbkey** in IGV is the same term as used in Galaxy, and you select **local IGV** display from Galaxy, your datasets can be loaded up all together into IGV! You can also just download all your files and not use Galaxy to host the data, but you’ll still need to configure IGV with your custom genome for the display if you need the genomic DNA sequence as the reference and plan to view all the files together. * * * Please give that a try and let us know if you need more help! 🙂 --- _[View the full topic](https://help.galaxyproject.org/t/bam-index-fasta-indexes-display-applications-custom-genome-builds-igv/16283)._