Frequently Asked Questions

Q1: I clicked icons on the JoGo website but encountered an error and couldn't open them.

To explore the JoGo haplotype dataset, you need to install the IGV (Integrative Genomics Viewer) software on your desktop.
You can download IGV from the Broad Institute website (Download IGV).
After downloading and installing IGV, make sure to launch the IGV application before clicking any icons on the JoGo website.
If you still encounter issues, please refer to the next question.

Q2: I have installed and launched IGV on my desktop, but clicking the JoGo icons still results in an error in my web browser.

This issue may occur if you have multiple instances of IGV running on your computer and you closed the first one.
By default, IGV communicates using port 60151.
If you open multiple instances of IGV, the second instance may not be able to use port 60151 (which is already being used by the first instance).
To resolve this, try logging out and back into your computer or rebooting your system.
If the problem persists, it may be caused by security software blocking port 60151.
In this case, you will need to contact your organization's network technical support team.

Q3: I have explored JoGo database and found interesting candidate for further analysis. To conclude the finding, furture analysis required. Is it possible to any collaboration for such kind of analysis?

Yes. Please contact us.

Q4: I was able to launch IGV. How do I use the software?

For general usage, please refer to the official iGVtutorials on YouTube, especially Sequencing Data Basics and Data Navigation Basics.

Q5: How can I create a GRCh38-aligned BAM to view together with JoGo data in IGV?

If you want to inspect your own sequencing reads alongside JoGo haplotype/Iso-Seq tracks in the Local Haplotype Explorer, you will need a coordinate-sorted and indexed BAM (or CRAM) aligned to the human reference GRCh38.

Reference genomes provided by JoGo:
• Long reads (ONT / PacBio): use hs38.fa (distributed as hs38.zip) – download here.
• Short reads (Illumina): use hs38DH.fa (GRCh38 with decoy/HLA) – download here.

Option A (GUI, no command line): You can use Galaxy’s BWA-MEM mapping tutorials to go from FASTQ to BAM entirely in the browser. Simply select GRCh38 (or upload hs38DH.fa) as the reference and download the sorted BAM and its index.

Option B (Illumina short reads; command line):
bwa index hs38DH.fa
bwa mem -t 16 hs38DH.fa sample_R1.fastq.gz sample_R2.fastq.gz > sample.sam
samtools view -bS sample.sam | samtools sort -o sample.sorted.bam
samtools index sample.sorted.bam
link to bwa software
(Optional: run Picard MarkDuplicates for downstream GATK pipelines.)

Option C (Long reads; PacBio HiFi; command line):
minimap2 -t 16 -ax map-hifi hs38.fa reads.fastq > aln.sam
samtools view -bS aln.sam | samtools sort -o aln.sorted.bam
samtools index aln.sorted.bam
link to minimap2 software

Option C (Long reads; ONT; command line):
minimap2 -t 16 -ax map-ont hs38.fa reads.fastq > aln.sam
samtools view -bS aln.sam | samtools sort -o aln.sorted.bam
samtools index aln.sorted.bam
link to minimap2 software

Open the BAM in IGV: Place the .bam and its .bai in the same folder, then load them in IGV after selecting the GRCh38 genome. CRAM is also supported if IGV has access to the same reference FASTA.

Q6: The content of JoGo database can used in commartial product?

For licensing condition as commertial product, please contact us.