UCSC Genome Browser Instructions

1. Xiphophorus 
2. UCSC genome browser 
3. Navigate the genome
4. Data visualization 
5. Data download

1. Xiphophorus 
Please visit the Xiphophorus Genetic Stock Center website (www.xiphophorus.txstate.edu/) for more details about Xiphophorus

2. UCSC genome browser 
The UCSC genome browser, implemented at the Xiphophorus genetic stock center, is a genome hub of the UCSC genome browser (https://genome.ucsc.edu/ (Genome Res. 2002 Jun;12(6):996-1006.). For a full tutorial of this platform, please refer to the UCSC genome browser website.

To visualize the X. maculatus genome, go to “My Data”->”Track Hubs”, select “My Hubs” and enter “https://viewer.xgsc.txstate.edu/data/ucsc_track_hub/hub.txt” in the search text box, and click “connect” button. 

The Genome Browser Gateway should show Xmac Hub Assembly to be Xiphophorus maculatus 5.0 (SMRT), click “GO” to launch the browser 

3. Navigate the genome
Use the “<” (move left) and “>” (move right) buttons to navigate chromosomes, and “zoom in” and “zoom out” buttons to expand or shrink a locus.

The genome database also allows other types of input to move to a specific locus:
-1 Transcript ID;
-2 Gene ID;
-3 Gene name;
-4 chromosome name and coordinates. For example: NC_036447.1:10,475,000-11,215,000 (note the “,” is required)

4. Data visualization 
The genome browser is launched with a gene model and associated dataset (i.e., RNA-Seq data: short RNA-Seq sequencing reads alignment; Multiple Alignment: comparative genomic data between X. maculatus to other fish biomedical models and human); user can use the drop-down menu to select the built-in dataset to display.

---Import data from workstation or user custom data server: 
To load user’s own data for visualization, datasets need to be processed into a certain format on a user’s local workstation or data server. The UCSC genome browser accepts multiple file formats, including bedGraph, GTF, PSL, BED, bigBed, WIG, bigGenePred, bigWig, BAM, VCF, MAF, BED detail, Personal Genome SNP, broadPeak, narrowPeak, and microarray (BED15). Here is an example of visualizing transcriptome .bam file (for data generated using different tool kits, please refer to their instruction). 

1. Alignment using tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml):  
   a. Building genome index: bowtiw2-build genome.fa database_index  
   b. Genome alignment: tophat2 -o output database_index pairend1.fastq pairend2.fastq

2. Indexing alignment file: samtools index output/accepted.bam 
To load the alignment file, click “My Data”, then “Custom Track”, select ”Choose File” and navigate to the folder/path where your data is stored. Data can also be provided via a URL. If users have a data server/data repository, providing the URL to the data will directly pull the data to genome browser.

---Import data from XGSC data server: 
The Xiphophorus Genetic Stock Center shares data with the research community. Currently, we share a few tissue specific RNA-Seq data. These data are available for download at https://viewer.xgsc.txstate.edu/data/SampleData/UCSC. To load sample data directly, click "My Data"->"Custom Track", and paste the URL of the data of interest into the dialog box. The data will appear as a track in the genome browser. We recommend this approach to visualize data instead of downloading them to your workstation or data server, unless you have special tasks to perform with the data. 

In the future, we plan to host Xiphophorus genetic data from the entire community. However, due to hardware limitations, we can only host selected datasets to share with the community at this time. If you are interested in sharing your data, especially RNA-Seq, ChIP-Seq, non-coding RNA data, please contact the XGSC staff/faculty. 

We are migrating to cloud based data processing and data sharing services. Upon server availability, we will provide bioinformatic tool kits and dedicated servers to carry out users' task. 

5. Data download 
X. hellerii chromosome assembly genome, X. couchianus chromosome assembly, X. maculatus chromosome assembly and contig assembly (.fasta) sequences and genome annotation (.gtf) are all available in “viewer.xgsc.txstate.edu/data” for download. The genome alignment data is also available in the /data directory. The multiple genome alignment was performed using lastz aligner and multiz-tba package. You can perform genome alignments between other species and X. maculatus using your favorite pipeline, or we can align your genome(s)-of-interest to Xiphophorus on request.