A first draft of the tutorial has been created and is ready for review!

While making this tutorial, I was thinking of all the file types someone might receive from a personal genomics company and made sure to explain how each one can be viewed in IGB. Are there any I missed?

We've also been discussing whether to include the section for 23andMe-specific data – I'm leaning towards including it.

temporary link: https://wiki.bioviz.org/confluence/pages/viewpage.action?pageId=68191401

Some general thoughts/suggestions:
BAM/CRAM section

• I would include a brief sentence describing what a BAM/CRAM is in layman's terms. Something like "the BAM/CRAM is a large file that contains the sequencing data of your DNA".
• Replace the word "directory" with "folder" so that it is easier for non computer people to understand.
• I would provide a specific region to zoom in on, some kind of gene or something and then tell them to Load Data. Include a picture of what it should look like so they can compare.

VCF section

• I would just copy/paste the instructions for loading the file instead of referring to the BAM/CRAM section. That way someone who is only interested in VCF doesn't have to read through two different sections.
• I would also provide a specific region to zoom in on and load the VCF and include an image showing what it should look like.

Convert raw genotyping data from 23andMe section

• This gets a bit tricky, but as far as I know (I have 23andMe data from 2013 up until 2024) they have always aligned their data to hg37 (build 37) of the human genome. So I wouldn't have IGB users click on the Mona Lisa as that would take them to hg38 (or whatever future version of the human genome comes out). They will need to select the H_sapiens_Feb_2009 genome version. However, there is the option in the SNP file converter to convert to the hg38 build of the human genome. It seems like it is still working, but I would lean towards just having the users use the hg37 genome build.
• If you did want to include example data or show an image (which I apparently did convert to hg38), you can use one of the example files from the Canvas IGB training module: https://canvas.instructure.com/courses/1164217/pages/intro-to-igb-data-visualization?module_item_id=20682655

Thank you for the temporary link! I've updated the tutorial according to these comments. Pictures are now included for the BAM/CRAM and VCF file sections. The VCF file section has steps outlined now, too. I also made some of the text throughout the tutorial more user-friendly as per your suggestions.

The link I've used for the VCF file section is not hosted by us, so there's always a risk that goes down without us noticing. Also, I opted to not include mention of the option to convert between hg37 and hg38 genome builds with SNP file converter. It seemed like that would get a bit confusing for the purposes of this tutorial.

Ready for another round of review!

I've finalized the last section of the CRAM tutorial with some general edits and added images. I think next step is to do a final review of the tutorial and release it to the User's Guide if it looks good.

I made a few minor text changes.

I think it should be ready to publish. If you had the time and felt like it, I think it could be helpful to add an image showing what the 23andMe SNP file would look like in IGB. I think it would also be helpful to include an image showing where the View icon and the Display in IGB button are in Galaxy, as I have gotten confused by this in the past.

I've added a image to the 23andMe section to demonstrate what that might look like! As for the Galaxy instructions, I've linked to another page in the User's Guide here which contains more details about that data viz process.

The tutorial has now been published. Closing ticket.